From 79d238907d0764bedee58672ac7b4838ff5046a1 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 20 Sep 2023 16:19:35 +0100 Subject: [PATCH 01/35] Ability to disregard duplicate runfolders. Allow to find a runfolder in 'analysis' or 'outgoing' in the presence of a duplicate runfolder in 'incoming'. The duplicates in 'incoming' are sometimes created by instruments well after the run was mirrored and the runfolder moved to 'analysis'. --- lib/npg_tracking/illumina/run/folder.pm | 16 ++++- t/60-illumina-runfolder.t | 80 ++++++++++++++++++++++++- 2 files changed, 92 insertions(+), 4 deletions(-) diff --git a/lib/npg_tracking/illumina/run/folder.pm b/lib/npg_tracking/illumina/run/folder.pm index c373bc0f..84789492 100644 --- a/lib/npg_tracking/illumina/run/folder.pm +++ b/lib/npg_tracking/illumina/run/folder.pm @@ -18,6 +18,9 @@ our $VERSION = '0'; with q{npg_tracking::illumina::run}; +# Top-level directory where instruments create runfolders +Readonly::Scalar my $INCOMING_DIR => q{/incoming/}; + # Directories created by Illumina software Readonly::Scalar my $DATA_DIR => q{Data}; Readonly::Scalar my $CONFIG_DIR => q{Config}; @@ -287,11 +290,18 @@ sub _get_path_from_glob_pattern { croak q{No paths to run folder found}; } - my %fs_inode_hash; #ignore multiple paths point to the same folder + my %fs_inode_hash; # ignore multiple paths point to the same folder @dir = grep { not $fs_inode_hash { join q(,), stat $_ }++ } @dir; - if ( @dir > 1 ) { - croak q{Ambiguous paths for run folder found: } . join qq{\n}, @dir; + # Ignore the case when some of the directories are in the /incoming/ + # folder - these are likely to be spurious directories created by + # instruments well after the run was mirrored and moved to /analysis/ + # or even to /outgoing/. + my @dir_not_incoming = grep { $_ !~ /$INCOMING_DIR/xms } @dir; + if (!@dir_not_incoming || (@dir_not_incoming > 1)) { + croak q{Ambiguous paths for run folder found: } . join qq{\n}, @dir; + } + @dir = @dir_not_incoming; } return shift @dir; diff --git a/t/60-illumina-runfolder.t b/t/60-illumina-runfolder.t index 41d5a51d..07ea02c5 100644 --- a/t/60-illumina-runfolder.t +++ b/t/60-illumina-runfolder.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 28; +use Test::More tests => 29; use Test::Exception; use Archive::Tar; use IO::File; @@ -224,4 +224,82 @@ subtest 'getting id_run from experiment name in run parameters' => sub { } }; +subtest 'duplicate runfolders' => sub { + plan tests => 9; + + my $staging = tempdir( CLEANUP => 1 ); + my $new_id_run = 898989; + for (qw(incoming analysis outgoing)) { + mkdir(catdir($staging, $_)); + } + my $rf_name = '230920_NV11_47885'; + my $run_row = $schema->resultset('Run')->create({ + id_run => $new_id_run, + id_instrument => 10, + id_instrument_format => 10, + team => 'A', + folder_name => $rf_name, + folder_path_glob => "$staging/*/" + }); + $run_row->set_tag(1, 'staging'); + + for (qw(analysis outgoing)) { + mkdir("$staging/$_/$rf_name"); + } + + my $rf_obj = npg_tracking::illumina::runfolder->new( + id_run => $new_id_run, npg_tracking_schema => $schema); + throws_ok { $rf_obj->runfolder_path() } + qr/Ambiguous paths for run folder found/, + 'error with a runfolder both in analysis and outgoing'; + + $rf_obj = npg_tracking::illumina::runfolder->new( + id_run => $new_id_run, npg_tracking_schema => $schema); + mkdir("$staging/incoming/$rf_name"); + throws_ok { $rf_obj->runfolder_path() } + qr/Ambiguous paths for run folder found/, + 'error with a runfolder in incoming, analysis and outgoing'; + + rmdir("$staging/outgoing/$rf_name"); + my $path; + $rf_obj = npg_tracking::illumina::runfolder->new( + id_run => $new_id_run, npg_tracking_schema => $schema); + lives_ok { $path = $rf_obj->runfolder_path() } + 'no error with a runfolder in both incoming and analysis'; + is($path, "$staging/analysis/$rf_name", + 'correct runfolder path is retrieved'); + + mkdir("$staging/outgoing/$rf_name"); + rmdir("$staging/analysis/$rf_name"); + $rf_obj = npg_tracking::illumina::runfolder->new( + id_run => $new_id_run, npg_tracking_schema => $schema); + lives_ok { $path = $rf_obj->runfolder_path() } + 'no error with a runfolder in both incoming and outgoing'; + is ($path, join(q[/], $staging, 'outgoing', $rf_name), + 'correct path is retrieved'); + + $staging = catdir($staging, 'incoming'); + $run_row->update({folder_path_glob => "$staging/*/"}); + for (qw(incoming analysis outgoing)) { + mkdir(catdir($staging, $_)); + } + for (qw(incoming outgoing)) { + mkdir("$staging/$_/$rf_name"); + } + + $rf_obj = npg_tracking::illumina::runfolder->new( + id_run => $new_id_run, npg_tracking_schema => $schema); + throws_ok { $rf_obj->runfolder_path() } + qr/Ambiguous paths for run folder found/, + 'error with multiple runfolders with paths in incoming'; + + rmdir("$staging/outgoing/$rf_name"); + $rf_obj = npg_tracking::illumina::runfolder->new( + id_run => $new_id_run, npg_tracking_schema => $schema); + lives_ok { $path = $rf_obj->runfolder_path() } + 'no error with a runfolder only in incoming'; + is ($path, join(q[/], $staging, 'incoming', $rf_name), + 'correct path is retrieved'); +}; + 1; From 71abfbb576c5847e6d9a30119aec0a3d256500d4 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 22 Sep 2023 09:34:22 +0100 Subject: [PATCH 02/35] Simplified samplesheet auto-generation code. Recently, the default LIMS driver type in samplesheet generation was changed to 'ml_warehouse'. Following this change, the code for auto-generation of MiSeq default samplesheets is now simplified to exclude an explicit creation of LIMS objects. --- lib/npg/samplesheet/auto.pm | 16 +++------------- 1 file changed, 3 insertions(+), 13 deletions(-) diff --git a/lib/npg/samplesheet/auto.pm b/lib/npg/samplesheet/auto.pm index 3a4b479d..bcc061e9 100644 --- a/lib/npg/samplesheet/auto.pm +++ b/lib/npg/samplesheet/auto.pm @@ -11,7 +11,6 @@ use File::Spec::Functions; use npg::samplesheet; use npg_tracking::Schema; use WTSI::DNAP::Warehouse::Schema; -use st::api::lims; use st::api::lims::samplesheet; with q(MooseX::Log::Log4perl); @@ -107,17 +106,10 @@ sub process { my $id_run = $r->id_run; $self->log->info('Considering ' . join q[,],$id_run,$r->instrument->name); - my $l = st::api::lims->new( - position => 1, - id_run => $id_run, - id_flowcell_lims => $r->batch_id, - driver_type => q(ml_warehouse), - mlwh_schema => $self->mlwh_schema + my $ss = npg::samplesheet->new( + run => $r, mlwh_schema => $self->mlwh_schema ); - - my $ss = npg::samplesheet->new(run => $r, lims => [$l]); - - my$o=$ss->output; + my $o = $ss->output; my $generate_new = 1; if(-e $o) { @@ -228,8 +220,6 @@ __END__ =item npg::samplesheet -=item st:api::lims - =item st::api::lims::samplesheet =item WTSI::DNAP::Warehouse::Schema From d0ed22d9074bd2d354385cabba301bcb03e5f72a Mon Sep 17 00:00:00 2001 From: mgcam Date: Tue, 26 Sep 2023 13:17:46 +0100 Subject: [PATCH 03/35] Drop xml fixtures in tests for samplesheet generation (#753) * Samplesheet generation tests - move to mlwh driver. Previously the tests uses XML feeds as a source of LIMS data. All production code is using mlwh database as a source of LIMS data. Amend tests to use mlwh data and the default ml_warehouse lims driver. Amended how an undefined sample public name is dealt with, i.e. converted an error to a warning and assigned a sensible fall-back value. Some samplesheets are generated without names of study owners, followers, etc. This is due to the fact that some studies do not have fixtures for user data. The database fixtures were generated from the current data, this explains multiple differences between the old and new content of the generated samplesheets. In some tests newer production batches were used instead of hand-crafted data. Deleted tests for old scenarios that do not exist in production any longer. Deleted tests that are duplicated by similar tests with more contemporary test data. * Deleted now redundant XML test fixtures --- MANIFEST | 151 +- lib/npg/samplesheet.pm | 4 +- t/47-samplesheet.t | 250 +- .../000-Sample.yml | 9768 +++++++++++++++++ .../000-Study.yml | 363 + .../100-IseqFlowcell.yml | 7054 ++++++++++++ .../100-StudyUser.yml | 37 + t/data/samplesheet/1control7libs_extended.csv | 10 - t/data/samplesheet/4pool4libs_extended.csv | 220 +- t/data/samplesheet/6946_extended.csv | 24 +- t/data/samplesheet/7007_extended.csv | 2 +- t/data/samplesheet/dual_index_default_new.csv | 50 + .../samplesheet/dual_index_extended_new.csv | 34 + t/data/samplesheet/st/batches/1.xml | 87 - t/data/samplesheet/st/batches/13994.xml | 107 - t/data/samplesheet/st/batches/14505.xml | 14 - t/data/samplesheet/st/batches/16537.xml | 51 - t/data/samplesheet/st/batches/16538.xml | 51 - t/data/samplesheet/st/batches/23798.xml | 939 -- t/data/samplesheet/st/projects/1238.xml | 37 - t/data/samplesheet/st/projects/1366.xml | 37 - t/data/samplesheet/st/projects/1422.xml | 37 - t/data/samplesheet/st/projects/521.xml | 37 - t/data/samplesheet/st/projects/678.xml | 37 - t/data/samplesheet/st/projects/714.xml | 37 - t/data/samplesheet/st/samples/1255141.xml | 2860 ----- t/data/samplesheet/st/samples/1289830.xml | 206 - t/data/samplesheet/st/samples/1289832.xml | 207 - t/data/samplesheet/st/samples/1289833.xml | 207 - t/data/samplesheet/st/samples/1289834.xml | 207 - t/data/samplesheet/st/samples/1289835.xml | 207 - t/data/samplesheet/st/samples/1289836.xml | 207 - t/data/samplesheet/st/samples/1289837.xml | 207 - t/data/samplesheet/st/samples/1289838.xml | 207 - t/data/samplesheet/st/samples/1289839.xml | 207 - t/data/samplesheet/st/samples/1289840.xml | 207 - t/data/samplesheet/st/samples/1289841.xml | 207 - t/data/samplesheet/st/samples/1289842.xml | 207 - t/data/samplesheet/st/samples/1289843.xml | 207 - t/data/samplesheet/st/samples/1392234.xml | 207 - t/data/samplesheet/st/samples/1392235.xml | 207 - t/data/samplesheet/st/samples/1392236.xml | 207 - t/data/samplesheet/st/samples/1392237.xml | 207 - t/data/samplesheet/st/samples/1392238.xml | 207 - t/data/samplesheet/st/samples/1660679.xml | 211 - t/data/samplesheet/st/samples/1660680.xml | 211 - t/data/samplesheet/st/samples/1694494.xml | 212 - t/data/samplesheet/st/samples/1694495.xml | 212 - t/data/samplesheet/st/samples/1694496.xml | 212 - t/data/samplesheet/st/samples/1694497.xml | 212 - t/data/samplesheet/st/samples/1694498.xml | 212 - t/data/samplesheet/st/samples/1694499.xml | 212 - t/data/samplesheet/st/samples/1706390.xml | 212 - t/data/samplesheet/st/samples/1706391.xml | 212 - t/data/samplesheet/st/samples/1706392.xml | 212 - t/data/samplesheet/st/samples/1706393.xml | 212 - t/data/samplesheet/st/samples/1706394.xml | 212 - t/data/samplesheet/st/samples/1706395.xml | 212 - t/data/samplesheet/st/samples/1706396.xml | 212 - t/data/samplesheet/st/samples/1706397.xml | 212 - t/data/samplesheet/st/samples/1706398.xml | 212 - t/data/samplesheet/st/samples/1706399.xml | 212 - t/data/samplesheet/st/samples/1706400.xml | 212 - t/data/samplesheet/st/samples/1706401.xml | 212 - t/data/samplesheet/st/samples/1706402.xml | 212 - t/data/samplesheet/st/samples/1706403.xml | 212 - t/data/samplesheet/st/samples/1706404.xml | 212 - t/data/samplesheet/st/samples/1706405.xml | 212 - t/data/samplesheet/st/samples/1706406.xml | 212 - t/data/samplesheet/st/samples/1706407.xml | 212 - t/data/samplesheet/st/samples/1706408.xml | 212 - t/data/samplesheet/st/samples/1706409.xml | 212 - t/data/samplesheet/st/samples/1706410.xml | 212 - t/data/samplesheet/st/samples/1706411.xml | 212 - t/data/samplesheet/st/samples/1706412.xml | 212 - t/data/samplesheet/st/samples/1706413.xml | 212 - t/data/samplesheet/st/samples/1706414.xml | 212 - t/data/samplesheet/st/samples/1706415.xml | 212 - t/data/samplesheet/st/samples/1706416.xml | 212 - t/data/samplesheet/st/samples/1706417.xml | 212 - 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t/data/samplesheet/st/samples/1706478.xml | 212 - t/data/samplesheet/st/samples/1706479.xml | 212 - t/data/samplesheet/st/samples/1706480.xml | 212 - t/data/samplesheet/st/samples/1706481.xml | 212 - t/data/samplesheet/st/samples/1706482.xml | 212 - t/data/samplesheet/st/samples/1706483.xml | 212 - t/data/samplesheet/st/samples/1706484.xml | 212 - t/data/samplesheet/st/samples/1706485.xml | 212 - t/data/samplesheet/st/samples/1712041.xml | 212 - t/data/samplesheet/st/studies/1697.xml | 195 - t/data/samplesheet/st/studies/198.xml | 181 - t/data/samplesheet/st/studies/1980.xml | 161 - t/data/samplesheet/st/studies/2239.xml | 221 - t/data/samplesheet/st/studies/2501.xml | 187 - t/data/samplesheet/st/studies/2658.xml | 185 - t/data/samplesheet/st/studies/521.xml | 171 - t/data/samplesheet/st/studies/700.xml | 175 - 157 files changed, 17540 insertions(+), 32217 deletions(-) create mode 100644 t/data/fixtures_lims_wh_samplesheet/000-Sample.yml create mode 100644 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t/data/samplesheet/st/samples/1706473.xml delete mode 100644 t/data/samplesheet/st/samples/1706474.xml delete mode 100644 t/data/samplesheet/st/samples/1706475.xml delete mode 100644 t/data/samplesheet/st/samples/1706476.xml delete mode 100644 t/data/samplesheet/st/samples/1706477.xml delete mode 100644 t/data/samplesheet/st/samples/1706478.xml delete mode 100644 t/data/samplesheet/st/samples/1706479.xml delete mode 100644 t/data/samplesheet/st/samples/1706480.xml delete mode 100644 t/data/samplesheet/st/samples/1706481.xml delete mode 100644 t/data/samplesheet/st/samples/1706482.xml delete mode 100644 t/data/samplesheet/st/samples/1706483.xml delete mode 100644 t/data/samplesheet/st/samples/1706484.xml delete mode 100644 t/data/samplesheet/st/samples/1706485.xml delete mode 100644 t/data/samplesheet/st/samples/1712041.xml delete mode 100644 t/data/samplesheet/st/studies/1697.xml delete mode 100644 t/data/samplesheet/st/studies/198.xml delete mode 100644 t/data/samplesheet/st/studies/1980.xml delete mode 100644 t/data/samplesheet/st/studies/2239.xml delete mode 100644 t/data/samplesheet/st/studies/2501.xml delete mode 100644 t/data/samplesheet/st/studies/2658.xml delete mode 100644 t/data/samplesheet/st/studies/521.xml delete mode 100644 t/data/samplesheet/st/studies/700.xml diff --git a/MANIFEST b/MANIFEST index 695e310e..6990c596 100644 --- a/MANIFEST +++ b/MANIFEST @@ -500,6 +500,10 @@ t/data/fixtures_stlims_wh/000-Study.yml t/data/fixtures_stlims_wh/100-IseqFlowcell.yml t/data/fixtures_stlims_wh/100-StudyUser.yml t/data/fixtures_stlims_wh/200-IseqProductMetric.yml +t/data/fixtures_lims_wh_samplesheet/000-Sample.yml +t/data/fixtures_lims_wh_samplesheet/000-Study.yml +t/data/fixtures_lims_wh_samplesheet/100-StudyUser.yml +t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml t/data/gaii/staging/IL3/incoming/100622_IL3_01234/this_run_is_not_complete_yet t/data/gaii/staging/IL5/incoming/not_a_dir t/data/gaii/staging/IL999/incoming/100622_IL3_01234/Recipe_GA2-PEM_2x76Cycle_v7.7.xml @@ -743,161 +747,18 @@ t/data/run_params/RunParameters.novaseq.xp.lite.xml t/data/samplesheet/samplesheet_7753.csv t/data/samplesheet/samplesheet_27483.csv t/data/samplesheet/samplesheet_33990.csv -t/data/samplesheet/1control7libs_extended.csv t/data/samplesheet/4pool4libs_extended.csv t/data/samplesheet/6946_extended.csv t/data/samplesheet/7007_extended.csv t/data/samplesheet/8pools_extended.csv t/data/samplesheet/dual_index_extended.csv +t/data/samplesheet/dual_index_default_new.csv +t/data/samplesheet/dual_index_extended_new.csv t/data/samplesheet/miseq_default.csv t/data/samplesheet/miseq_default_dual_index.csv t/data/samplesheet/miseq_extended.csv t/data/samplesheet/multilane.csv t/data/samplesheet/novaseq_multirun.csv -t/data/samplesheet/st/batches/1.xml -t/data/samplesheet/st/batches/13994.xml -t/data/samplesheet/st/batches/14505.xml -t/data/samplesheet/st/batches/16537.xml -t/data/samplesheet/st/batches/16538.xml -t/data/samplesheet/st/batches/23798.xml -t/data/samplesheet/st/projects/1238.xml -t/data/samplesheet/st/projects/1366.xml -t/data/samplesheet/st/projects/1422.xml -t/data/samplesheet/st/projects/521.xml -t/data/samplesheet/st/projects/678.xml -t/data/samplesheet/st/projects/714.xml -t/data/samplesheet/st/samples/1255141.xml -t/data/samplesheet/st/samples/1289830.xml -t/data/samplesheet/st/samples/1289832.xml -t/data/samplesheet/st/samples/1289833.xml -t/data/samplesheet/st/samples/1289834.xml -t/data/samplesheet/st/samples/1289835.xml -t/data/samplesheet/st/samples/1289836.xml -t/data/samplesheet/st/samples/1289837.xml -t/data/samplesheet/st/samples/1289838.xml -t/data/samplesheet/st/samples/1289839.xml -t/data/samplesheet/st/samples/1289840.xml -t/data/samplesheet/st/samples/1289841.xml -t/data/samplesheet/st/samples/1289842.xml -t/data/samplesheet/st/samples/1289843.xml -t/data/samplesheet/st/samples/1392234.xml -t/data/samplesheet/st/samples/1392235.xml -t/data/samplesheet/st/samples/1392236.xml -t/data/samplesheet/st/samples/1392237.xml -t/data/samplesheet/st/samples/1392238.xml -t/data/samplesheet/st/samples/1660679.xml -t/data/samplesheet/st/samples/1660680.xml -t/data/samplesheet/st/samples/1694494.xml -t/data/samplesheet/st/samples/1694495.xml -t/data/samplesheet/st/samples/1694496.xml -t/data/samplesheet/st/samples/1694497.xml -t/data/samplesheet/st/samples/1694498.xml -t/data/samplesheet/st/samples/1694499.xml -t/data/samplesheet/st/samples/1706390.xml -t/data/samplesheet/st/samples/1706391.xml -t/data/samplesheet/st/samples/1706392.xml -t/data/samplesheet/st/samples/1706393.xml -t/data/samplesheet/st/samples/1706394.xml -t/data/samplesheet/st/samples/1706395.xml -t/data/samplesheet/st/samples/1706396.xml -t/data/samplesheet/st/samples/1706397.xml -t/data/samplesheet/st/samples/1706398.xml -t/data/samplesheet/st/samples/1706399.xml -t/data/samplesheet/st/samples/1706400.xml -t/data/samplesheet/st/samples/1706401.xml -t/data/samplesheet/st/samples/1706402.xml -t/data/samplesheet/st/samples/1706403.xml -t/data/samplesheet/st/samples/1706404.xml -t/data/samplesheet/st/samples/1706405.xml -t/data/samplesheet/st/samples/1706406.xml -t/data/samplesheet/st/samples/1706407.xml -t/data/samplesheet/st/samples/1706408.xml -t/data/samplesheet/st/samples/1706409.xml -t/data/samplesheet/st/samples/1706410.xml -t/data/samplesheet/st/samples/1706411.xml -t/data/samplesheet/st/samples/1706412.xml -t/data/samplesheet/st/samples/1706413.xml -t/data/samplesheet/st/samples/1706414.xml -t/data/samplesheet/st/samples/1706415.xml -t/data/samplesheet/st/samples/1706416.xml -t/data/samplesheet/st/samples/1706417.xml -t/data/samplesheet/st/samples/1706418.xml -t/data/samplesheet/st/samples/1706419.xml -t/data/samplesheet/st/samples/1706420.xml -t/data/samplesheet/st/samples/1706421.xml -t/data/samplesheet/st/samples/1706422.xml -t/data/samplesheet/st/samples/1706423.xml -t/data/samplesheet/st/samples/1706424.xml -t/data/samplesheet/st/samples/1706425.xml -t/data/samplesheet/st/samples/1706426.xml -t/data/samplesheet/st/samples/1706427.xml -t/data/samplesheet/st/samples/1706428.xml -t/data/samplesheet/st/samples/1706429.xml -t/data/samplesheet/st/samples/1706430.xml -t/data/samplesheet/st/samples/1706431.xml -t/data/samplesheet/st/samples/1706432.xml -t/data/samplesheet/st/samples/1706433.xml -t/data/samplesheet/st/samples/1706434.xml -t/data/samplesheet/st/samples/1706435.xml -t/data/samplesheet/st/samples/1706436.xml -t/data/samplesheet/st/samples/1706437.xml -t/data/samplesheet/st/samples/1706438.xml -t/data/samplesheet/st/samples/1706439.xml -t/data/samplesheet/st/samples/1706440.xml -t/data/samplesheet/st/samples/1706441.xml -t/data/samplesheet/st/samples/1706442.xml -t/data/samplesheet/st/samples/1706443.xml -t/data/samplesheet/st/samples/1706444.xml -t/data/samplesheet/st/samples/1706445.xml -t/data/samplesheet/st/samples/1706446.xml -t/data/samplesheet/st/samples/1706447.xml -t/data/samplesheet/st/samples/1706448.xml -t/data/samplesheet/st/samples/1706449.xml -t/data/samplesheet/st/samples/1706450.xml -t/data/samplesheet/st/samples/1706451.xml -t/data/samplesheet/st/samples/1706452.xml -t/data/samplesheet/st/samples/1706453.xml -t/data/samplesheet/st/samples/1706454.xml -t/data/samplesheet/st/samples/1706455.xml -t/data/samplesheet/st/samples/1706456.xml -t/data/samplesheet/st/samples/1706457.xml -t/data/samplesheet/st/samples/1706458.xml -t/data/samplesheet/st/samples/1706459.xml -t/data/samplesheet/st/samples/1706460.xml -t/data/samplesheet/st/samples/1706461.xml -t/data/samplesheet/st/samples/1706462.xml -t/data/samplesheet/st/samples/1706463.xml -t/data/samplesheet/st/samples/1706464.xml -t/data/samplesheet/st/samples/1706465.xml -t/data/samplesheet/st/samples/1706466.xml -t/data/samplesheet/st/samples/1706467.xml -t/data/samplesheet/st/samples/1706468.xml -t/data/samplesheet/st/samples/1706469.xml -t/data/samplesheet/st/samples/1706470.xml -t/data/samplesheet/st/samples/1706471.xml -t/data/samplesheet/st/samples/1706472.xml -t/data/samplesheet/st/samples/1706473.xml -t/data/samplesheet/st/samples/1706474.xml -t/data/samplesheet/st/samples/1706475.xml -t/data/samplesheet/st/samples/1706476.xml -t/data/samplesheet/st/samples/1706477.xml -t/data/samplesheet/st/samples/1706478.xml -t/data/samplesheet/st/samples/1706479.xml -t/data/samplesheet/st/samples/1706480.xml -t/data/samplesheet/st/samples/1706481.xml -t/data/samplesheet/st/samples/1706482.xml -t/data/samplesheet/st/samples/1706483.xml -t/data/samplesheet/st/samples/1706484.xml -t/data/samplesheet/st/samples/1706485.xml -t/data/samplesheet/st/samples/1712041.xml -t/data/samplesheet/st/studies/1697.xml -t/data/samplesheet/st/studies/198.xml -t/data/samplesheet/st/studies/1980.xml -t/data/samplesheet/st/studies/2239.xml -t/data/samplesheet/st/studies/2501.xml -t/data/samplesheet/st/studies/2658.xml -t/data/samplesheet/st/studies/521.xml -t/data/samplesheet/st/studies/700.xml t/data/st_api_lims_new/st/assets/3033734.xml t/data/st_api_lims_new/st/assets/3111688.xml t/data/st_api_lims_new/st/batches/12141.xml diff --git a/lib/npg/samplesheet.pm b/lib/npg/samplesheet.pm index 4f7d626c..e80fab86 100755 --- a/lib/npg/samplesheet.pm +++ b/lib/npg/samplesheet.pm @@ -284,11 +284,11 @@ sub _build__limsreflist { foreach my $attr (qw/library_id sample_publishable_name/) { my $value = _csv_compatible_value($tmpl->$attr); if (!$value) { - croak sprintf '%s is not available for position %i %s', + carp sprintf '%s is not available for position %i %s', $attr, $tmpl->position, defined $tmpl->tag_index ? 'tag index ' . $tmpl->tag_index : q[]; } - if ($self->mkfastq) { + if (!$value || $self->mkfastq) { # when making a samplesheet for mkfastq, replace value by run_position $value = $self->id_run . q[_] . $tmpl->position; if($self->_index_read) { diff --git a/t/47-samplesheet.t b/t/47-samplesheet.t index 4b88dea3..d27e1f7f 100644 --- a/t/47-samplesheet.t +++ b/t/47-samplesheet.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 13; +use Test::More tests => 12; use Test::LongString; use Test::Exception; use File::Slurp; @@ -19,35 +19,14 @@ my $schema = t::dbic_util->new->test_schema(); my $class = Moose::Meta::Class->create_anon_class(roles=>[qw/npg_testing::db/]); my $mlwh_schema = $class->new_object({})->create_test_db( - q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh] + q[WTSI::DNAP::Warehouse::Schema], q[t/data/fixtures_lims_wh_samplesheet] ); local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q(t/data/samplesheet); my $dir = tempdir( CLEANUP => 1 ); -subtest 'object creation' => sub { - plan tests => 8; - - my $result = q(); - dies_ok { npg::samplesheet->new( lims_driver_type=>'xml', repository=>$dir, output=>\$result)->process } - 'sample sheet process fails when neither run object nor id_run given'; - - my $ss; - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } 'sample sheet object - no output provided'; - cmp_ok($ss->output, 'eq', '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS0001309-300.csv', 'default output location (with zeroes trimmed appropriately)'); - is($ss->lims->[0]->driver_type, 'xml', 'xml driver is used'); - - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946); } 'sample sheet object - no output provided'; - cmp_ok($ss->output, 'eq', '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/000000000-A0616.csv', 'default output location'); - - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } 'sample sheet object - no output provided'; - my $orig_flowcell_id = $ss->run->flowcell_id; - $ss->run->flowcell_id(q(MS2000132-500V2)); - cmp_ok($ss->output, 'eq', '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS2000132-500V2.csv', 'default output location copes with V2 MiSeq cartirdges/reagent kits'); -}; - -subtest 'error on an unknown driver types' => sub { +subtest 'error on an unknown driver type' => sub { plan tests => 1; throws_ok { @@ -55,6 +34,7 @@ subtest 'error on an unknown driver types' => sub { lims_driver_type => 'foo', repository => $dir, npg_tracking_schema => $schema, + mlwh_schema => $mlwh_schema, id_run => 7007)->lims() } qr/Lazy-build for driver type foo is not inplemented/, 'error with the driver type for which LIMS objects cannot be built'; @@ -63,10 +43,6 @@ subtest 'error on an unknown driver types' => sub { subtest 'simple tests for the default driver' => sub { plan tests => 2; - my $run_row = $schema->resultset('Run')->find(7007); - my $current_batch_id = $run_row->batch_id; - $run_row->update({batch_id => 57543}); - my $ss = npg::samplesheet->new( repository => $dir, npg_tracking_schema => $schema, @@ -76,8 +52,37 @@ subtest 'simple tests for the default driver' => sub { is ($ss->lims_driver_type, 'ml_warehouse', 'correct default driver type'); my $lims = $ss->lims(); is (@{$lims}, 1, 'LIMS data for 1 lane is built'); +}; - $run_row->update({batch_id => $current_batch_id}); +subtest 'object creation' => sub { + plan tests => 7; + + my $result = q(); + dies_ok { npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, output=>\$result)->process } + 'samplesheet process fails when neither run object nor id_run given'; + + my $ss; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } + 'samplesheet object - no output provided'; + cmp_ok($ss->output, 'eq', + '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS0001309-300.csv', + 'default output location (with zeroes trimmed appropriately)'); + + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946); } + 'samplesheet object - no output provided'; + cmp_ok($ss->output, 'eq', + '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/000000000-A0616.csv', + 'default output location'); + + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007); } 'samplesheet object - no output provided'; + my $orig_flowcell_id = $ss->run->flowcell_id; + $ss->run->flowcell_id(q(MS2000132-500V2)); + cmp_ok($ss->output, 'eq', + '/nfs/sf49/ILorHSorMS_sf49/samplesheets/wibble/MS2000132-500V2.csv', + 'default output location copes with V2 MiSeq cartirdges/reagent kits'); }; subtest 'values conversion' => sub { @@ -125,20 +130,24 @@ Chemistry,Default,, ,,, [Data],,, Sample_ID,Sample_Name,GenomeFolder, -3789277,Strongyloides ratti,, +3789277,ERS092590,, RESULT_7007 $expected_result_7007 =~ s/\n/\r\n/smg; my $ss; my $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007, output=>\$result); } 'sample sheet object for unplexed paired run'; - lives_ok { $ss->process(); } ' sample sheet generated'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>7007, output=>\$result); } + 'samplesheet object for unplexed paired run'; + lives_ok { $ss->process(); } ' samplesheet generated'; is_string($result, $expected_result_7007); my $run = $schema->resultset(q(Run))->find(7007); $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, run=>$run, output=>\$result); } 'sample sheet object from run object - no id_run given'; - lives_ok { $ss->process(); } ' sample sheet generated'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, run=>$run, output=>\$result); } + 'samplesheet object from run object - no id_run given'; + lives_ok { $ss->process(); } ' samplesheet generated'; is_string($result, $expected_result_7007); }; @@ -147,7 +156,9 @@ subtest 'default samplesheet for a plexed paired run' => sub { my $ss; my $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, output=>\$result); } 'samplesheet object for plexed paired run'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, + id_run=>6946, output=>\$result); } 'samplesheet object for plexed paired run'; my $expected_result = << 'RESULT_6946'; [Header],,,, Investigator Name,mq1,,, @@ -181,7 +192,7 @@ Sample_ID,Sample_Name,GenomeFolder,Index, 3789289,Homo sapiens,,CTTGTACT, RESULT_6946 $expected_result =~ s/\n/\r\n/smg; - lives_ok { $ss->process(); } ' sample sheet generated'; + lives_ok { $ss->process(); } 'samplesheet generated'; is_string($result, $expected_result); }; @@ -190,7 +201,9 @@ subtest 'default samplesheet for a plexed paired run with reference fallback' => my $ss; my $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>7825, output=>\$result); } 'sample sheet object for plexed paired run'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema => $mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>7825, + output=>\$result); } 'samplesheet object for plexed paired run'; my $expected_result = << 'RESULT_7825'; [Header],,,, Investigator Name,nh4,,, @@ -217,141 +230,84 @@ Sample_ID,Sample_Name,GenomeFolder,Index, 4894526,PfIT_SOLiD5500_5kb,,TAGCTTGTAT, RESULT_7825 $expected_result =~ s/\n/\r\n/smg; - lives_ok { $ss->process(); } ' sample sheet generated'; - is_string($result, $expected_result, 'PhiX used as fall back reference'); + lives_ok { $ss->process(); } 'samplesheet generated'; + is_string($result, $expected_result, 'PhiX used as fall-back reference'); }; -subtest 'default samplesheet, mkfastq option enabled' => sub { - plan tests => 3; +subtest 'default and mkfastq samplesheets for dual index' => sub { + plan tests => 10; - # with the mkfastq option we get an extra leading column, Lane - my $ss; + my $run_6946 = $schema->resultset('Run')->find(6946); + my $batch_id = $run_6946->batch_id; + $schema->resultset('Run')->find(6946)->update({batch_id => 76873}); my $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>7826, mkfastq => 1, output=>\$result); } - 'sample sheet object mkfastq'; - my $expected_result = << 'RESULT_mkfastq'; -[Header],,,,, -Investigator Name,nh4,,,, -Project Name,Mate Pair R%26D,,,, -Experiment Name,7826,,,, -Date,2012-04-03T16:39:48,,,, -Workflow,GenerateFASTQ,,,, -Chemistry,Amplicon,,,, -,,,,, -[Reads],,,,, -75,,,,, -8,,,,, -,,,,, -[Settings],,,,, -,,,,, -[Manifests],,,,, -,,,,, -[Data],,,,, -Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2, -1,7826_1_ATCACGTTATAAAAAA,7826_1_ATCACGTTATAAAAAA,,ATCACGTT,ATAAAAAA, -1,7826_1_CGATGTTTATTTTTTT,7826_1_CGATGTTTATTTTTTT,,CGATGTTT,ATTTTTTT, -1,7826_1_ACTTGATGATCCCCCC,7826_1_ACTTGATGATCCCCCC,,ACTTGATG,ATCCCCCC, -1,7826_1_GATCAGCGATGGGGGG,7826_1_GATCAGCGATGGGGGG,,GATCAGCG,ATGGGGGG, -1,7826_1_TAGCTTGTATACACGT,7826_1_TAGCTTGTATACACGT,,TAGCTTGT,ATACACGT, -RESULT_mkfastq - $expected_result =~ s/\n/\r\n/smg; - lives_ok { $ss->process(); } ' sample sheet generated'; - is_string($result, $expected_result, 'mkfastq created'); -}; - -subtest 'default samplesheet for dual index' => sub { - plan tests => 3; - my $ss; - my $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>7826, output=>\$result); } 'sample sheet object for dual index'; - my $expected_result = << 'RESULT_7826'; -[Header],,,, -Investigator Name,nh4,,, -Project Name,Mate Pair R%26D,,, -Experiment Name,7826,,, -Date,2012-04-03T16:39:48,,, -Workflow,GenerateFASTQ,,, -Chemistry,Amplicon,,, -,,,, -[Reads],,,, -75,,,, -8,,,, -,,,, -[Settings],,,, -,,,, -[Manifests],,,, -,,,, -[Data],,,, -Sample_ID,Sample_Name,GenomeFolder,Index,Index2, -4894529,Mouse_test_3kb,,ATCACGTT,ATAAAAAA, -4894528,Tetse_3kb,,CGATGTTT,ATTTTTTT, -4894527,PfIT_454_5kb,,ACTTGATG,ATCCCCCC, -4894525,PfIT_Sanger_5kb,,GATCAGCG,ATGGGGGG, -4894526,PfIT_SOLiD5500_5kb,,TAGCTTGT,ATACACGT, -RESULT_7826 - $expected_result =~ s/\n/\r\n/smg; - lives_ok { $ss->process(); } ' sample sheet generated'; - is_string($result, $expected_result, 'Dual indexes created'); + lives_ok { $ss = npg::samplesheet->new(mlwh_schema=>$mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, output=>\$result) } + 'default samplesheet object for a dual index run'; + ok($ss->_dual_index, 'dual index from two indexes in LIMs'); + lives_ok { $ss->process(); } 'samplesheet generated'; + is_string($result, read_file('t/data/samplesheet/dual_index_default_new.csv')); + + $result = q(); + lives_ok { $ss = npg::samplesheet->new(mlwh_schema=>$mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, + mkfastq => 1, output=>\$result) } 'samplesheet object mkfastq'; + lives_ok { $ss->process(); } 'samplesheet generated'; + # With the mkfastq option we get an extra leading column, Lane. + my @lines = map { $_ =~ s/\s\Z//g; $_ } grep { $_ =~ /\A1,/} split qq[\n], $result; + is (scalar @lines, 32, '32 sample lines'); + is ($lines[0], + q[1,6946_1_CGTGACACTTATTGCG,6946_1_CGTGACACTTATTGCG,,CGTGACAC,TTATTGCG,]); + is ($lines[1], + q[1,6946_1_ACTTAGAGCTCCATAA,6946_1_ACTTAGAGCTCCATAA,,ACTTAGAG,CTCCATAA,]); + is ($lines[31], + q[1,6946_1_GTAAGATGAAAGGCTG,6946_1_GTAAGATGAAAGGCTG,,GTAAGATG,AAAGGCTG,]); + + $schema->resultset('Run')->find(6946)->update({batch_id => $batch_id}); }; subtest 'extended samplesheets' => sub { - plan tests => 23; + plan tests => 16; my $ss; my $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, extend => 1, id_run=>7007, output=>\$result); } 'extended sample sheet object for unplexed paired run'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema=>$mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, extend => 1, + id_run=>7007, output=>\$result); } + 'extended samplesheet object for unplexed paired run'; ok(!$ss->_dual_index, 'no dual index'); - lives_ok { $ss->process(); } ' sample sheet generated'; + lives_ok { $ss->process(); } 'samplesheet generated'; is_string($result, read_file('t/data/samplesheet/7007_extended.csv')); $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, extend => 1, output=>\$result); } 'extended sample sheet object for plexed paired run'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema=>$mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, + extend => 1, output=>\$result); } + 'extended samplesheet object for plexed paired run'; ok(!$ss->_dual_index, 'no dual index'); - lives_ok { $ss->process(); } ' sample sheet generated'; + lives_ok { $ss->process(); } 'samplesheet generated'; is_string($result, read_file('t/data/samplesheet/6946_extended.csv')); - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q[t/data/test45]; - # assign batch_id for run 3905 - one control lane and 7 libraries - $schema->resultset('Run')->find(6946)->update({batch_id => 4775}); - - $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, extend => 1, output=>\$result); } - 'extended sample sheet object for unplexed paired 8 lane run with a control lane'; - lives_ok { $ss->process(); } 'sample sheet generated'; - is_string($result, read_file('t/data/samplesheet/1control7libs_extended.csv')); - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q[t/data/test45]; - # assign batch_id for run 7690 - 8 pools - $schema->resultset('Run')->find(6946)->update({batch_id => 16249}); - - $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, extend => 1, output=>\$result); } - 'extended sample sheet object for plexed paired 8 lane run'; - ok(!$ss->_dual_index, 'no dual index'); - lives_ok { $ss->process(); } 'sample sheet generated'; - is_string($result, read_file('t/data/samplesheet/8pools_extended.csv')); - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q[t/data/samplesheet]; - # assign batch_id for run 11114 - 4 pools 4 libs $schema->resultset('Run')->find(6946)->update({batch_id => 23798}); - $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, extend => 1, output=>\$result); } - 'extended sample sheet object for plexed paired run with both pool and library lanes'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema=>$mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, + extend => 1, output=>\$result); } + 'extended samplesheet object for a dual index recorded as a single index'; ok($ss->_dual_index, 'dual index from a 16 char first index'); - lives_ok { $ss->process(); } 'sample sheet generated'; + lives_ok { $ss->process(); } 'samplesheet generated'; is_string($result, read_file('t/data/samplesheet/4pool4libs_extended.csv')); - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q[t/data/samplesheet]; - $schema->resultset('Run')->find(6946)->update({batch_id => 1,}); - + $schema->resultset('Run')->find(6946)->update({batch_id => 76873}); $result = q(); - lives_ok { $ss = npg::samplesheet->new(lims_driver_type=>'xml', repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, extend => 1, output=>\$result); } - 'extended sample sheet object for plexed paired run with both pool and library lanes'; + lives_ok { $ss = npg::samplesheet->new(mlwh_schema=>$mlwh_schema, + repository=>$dir, npg_tracking_schema=>$schema, id_run=>6946, + extend => 1, output=>\$result); } + 'extended samplesheet object for a dal index run'; ok($ss->_dual_index, 'dual index from two indexes in LIMs'); - lives_ok { $ss->process(); } 'sample sheet generated'; - is_string($result, read_file('t/data/samplesheet/dual_index_extended.csv')); + lives_ok { $ss->process(); } 'samplesheet generated'; + is_string($result, read_file('t/data/samplesheet/dual_index_extended_new.csv')); }; subtest 'samplesheets for data for multiple runs' => sub { diff --git a/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml b/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml new file mode 100644 index 00000000..95a25c9e --- /dev/null +++ b/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml @@ -0,0 +1,9768 @@ +--- +- accession_number: ERS092590 + age: ~ + cell_type: ~ + cohort: ~ + common_name: Strongyloides ratti + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 13:46:23 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: infective larvae L3 + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: High AT + gender: Mixed + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289830 + id_sample_tmp: 1271608 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: SriL3_66K_212889 + organism: Strongyloides ratti + organism_part: whole + phenotype: ~ + public_name: Strongyloides ratti + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Strongyloides_ratti (20100601) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: ED321 + subject: ~ + supplier_name: ~ + taxon_id: 34506 + time_point: ~ + treatment: ~ + uuid_sample_lims: 673165ec-f8c6-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Salmonella pullorum + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:31 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289832 + id_sample_tmp: 1271610 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: sp200shear + organism: Salmonella pullorum + organism_part: ~ + phenotype: ~ + public_name: Salmonella pullorum + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Salmonella_pullorum (449_87) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: 449_87 + subject: ~ + supplier_name: ~ + taxon_id: 590 + time_point: ~ + treatment: ~ + uuid_sample_lims: b51b4966-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Bordetella Pertussis + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:32 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: High GC + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289833 + id_sample_tmp: 1271611 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: bp200shear + organism: Bordetella Pertussis + organism_part: ~ + phenotype: ~ + public_name: Bordetella Pertussis + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Bordetella_pertussis (ST24) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: Bpst24 + subject: ~ + supplier_name: ~ + taxon_id: 520 + time_point: ~ + treatment: ~ + uuid_sample_lims: b5760fb8-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Plasmodium Falciparum + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:32 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: High AT + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289834 + id_sample_tmp: 1271612 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: 3D7200shear + organism: Plasmodium Falciparum + organism_part: ~ + phenotype: ~ + public_name: Plasmodium Falciparum + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Plasmodium_falciparum (3D7) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: 3D7 + subject: ~ + supplier_name: ~ + taxon_id: 5820 + time_point: ~ + treatment: ~ + uuid_sample_lims: b589b0cc-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Human + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:32 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289835 + id_sample_tmp: 1271613 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: human200shear + organism: Homo sapiens + organism_part: ~ + phenotype: ~ + public_name: Homo sapiens + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Homo_sapiens (GRCh37_53) DO_NOT_USE + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: colo_829 + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: b5e1b402-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Salmonella pullorum + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:33 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289836 + id_sample_tmp: 1271614 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: sp300shear + organism: Salmonella pullorum + organism_part: ~ + phenotype: ~ + public_name: Salmonella pullorum + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Salmonella_pullorum (449_87) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: 449_87 + subject: ~ + supplier_name: ~ + taxon_id: 590 + time_point: ~ + treatment: ~ + uuid_sample_lims: b5f4757e-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Bordetella Pertussis + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:33 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: High GC + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289837 + id_sample_tmp: 1271615 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: bp300shear + organism: Bordetella Pertussis + organism_part: ~ + phenotype: ~ + public_name: Bordetella Pertussis + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Bordetella_pertussis (ST24) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: Bpst24 + subject: ~ + supplier_name: ~ + taxon_id: 520 + time_point: ~ + treatment: ~ + uuid_sample_lims: b6064740-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Plasmodium Falciparum + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:33 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: High AT + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289838 + id_sample_tmp: 1271616 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: 3D7300shear + organism: Plasmodium Falciparum + organism_part: ~ + phenotype: ~ + public_name: Plasmodium Falciparum + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Plasmodium_falciparum (3D7) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: 3D7 + subject: ~ + supplier_name: ~ + taxon_id: 5820 + time_point: ~ + treatment: ~ + uuid_sample_lims: b65db606-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Human + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:33 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289839 + id_sample_tmp: 1271617 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: human300shear + organism: Homo sapiens + organism_part: ~ + phenotype: ~ + public_name: Homo sapiens + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Homo_sapiens (GRCh37_53) DO_NOT_USE + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: colo_829 + subject: ~ + supplier_name: ~ + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: b6790546-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Salmonella pullorum + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:34 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: Genomic + donor_id: ~ + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: Neutral + gender: ~ + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 1289840 + id_sample_tmp: 1271618 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-12 19:52:46 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: sp400shear + organism: Salmonella pullorum + organism_part: ~ + phenotype: ~ + public_name: Salmonella pullorum + purification_method: ~ + purified: ~ + recorded_at: 2021-04-12 20:34:05 + reference_genome: Salmonella_pullorum (449_87) + replicate: ~ + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: 449_87 + subject: ~ + supplier_name: ~ + taxon_id: 590 + time_point: ~ + treatment: ~ + uuid_sample_lims: b694245c-f8cc-11e0-8838-68b59976a382 +- accession_number: ~ + age: ~ + cell_type: ~ + cohort: ~ + common_name: Bordetella Pertussis + compound: ~ + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: ~ + created: 2011-10-17 14:31:34 + customer_measured_concentration: ~ + customer_measured_volume: ~ + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: genomic DNA + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: 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concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: N/A + created: 2013-09-25 09:10:09 + customer_measured_concentration: ~ + customer_measured_volume: N/A + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female + developmental_stage: embryonic stem cell line + disease: N/A + disease_state: N/A + dna_source: Cell Line + donor_id: ~ + dose: N/A + ethnicity: N/A + extraction_method: ~ + father: C57BL/6Ncr + gc_content: Neutral + gender: Male + genotype: G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female + geographical_region: N/A + growth_condition: alternative 2i/LIF + id_lims: SQSCP + id_sample_lims: 1706418 + id_sample_tmp: 1685090 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:32:06 + 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purified: ~ + recorded_at: 2021-04-12 21:33:23 + reference_genome: Mus_musculus (NCBIm37) + replicate: 30 + sample_type: ~ + sample_visibility: Hold + sanger_sample_id: ~ + sibling: ~ + storage_conditions: ~ + strain: G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female + subject: N/A + supplier_name: ~ + taxon_id: 10090 + time_point: N/A + treatment: N/A + uuid_sample_lims: 47427e30-25c2-11e3-96eb-68b59976a382 +- accession_number: ERS351261 + age: N/A + cell_type: ESC + cohort: ~ + common_name: Mus Musculus + compound: N/A + concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: N/A + created: 2013-09-25 09:10:10 + customer_measured_concentration: ~ + customer_measured_volume: N/A + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 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concentration_determined_by: ~ + consent_withdrawn: 0 + control: ~ + control_type: ~ + country_of_origin: N/A + created: 2013-09-25 09:10:12 + customer_measured_concentration: ~ + customer_measured_volume: N/A + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female + developmental_stage: embryonic stem cell line + disease: N/A + disease_state: N/A + dna_source: Cell Line + donor_id: ~ + dose: N/A + ethnicity: N/A + extraction_method: ~ + father: C57BL/6Ncr + gc_content: Neutral + gender: Male + genotype: G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female + geographical_region: N/A + growth_condition: alternative 2i/LIF + id_lims: SQSCP + id_sample_lims: 1706441 + id_sample_tmp: 1685113 + immunoprecipitate: N/A + is_resubmitted: ~ + last_updated: 2021-04-12 20:32:06 + 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control: ~ + control_type: ~ + country_of_origin: ~ + created: 2020-02-26 17:01:14 + customer_measured_concentration: ~ + customer_measured_volume: 20 + date_of_consent_withdrawn: ~ + date_of_sample_collection: ~ + date_of_sample_extraction: ~ + deleted_at: ~ + description: ~ + developmental_stage: ~ + disease: ~ + disease_state: ~ + dna_source: ~ + donor_id: PD41305k_185 + dose: ~ + ethnicity: ~ + extraction_method: ~ + father: ~ + gc_content: ~ + gender: Male + genotype: ~ + geographical_region: ~ + growth_condition: ~ + id_lims: SQSCP + id_sample_lims: 4396733 + id_sample_tmp: 4339317 + immunoprecipitate: ~ + is_resubmitted: ~ + last_updated: 2021-04-13 01:03:50 + marked_as_consent_withdrawn_by: ~ + mother: ~ + name: 6133STDY8786714 + organism: ~ + organism_part: ~ + phenotype: Blood + public_name: PD41305k_185 + purification_method: ~ + purified: ~ + recorded_at: 2021-04-13 12:07:20 + reference_genome: ~ + replicate: ~ + sample_type: ~ + sample_visibility: ~ + sanger_sample_id: 6133STDY8786714 + sibling: ~ + storage_conditions: ~ + strain: ~ + subject: ~ + supplier_name: PD41305k_185 + taxon_id: 9606 + time_point: ~ + treatment: ~ + uuid_sample_lims: 99276e32-58b9-11ea-9228-fa163e9d6485 + diff --git a/t/data/fixtures_lims_wh_samplesheet/000-Study.yml b/t/data/fixtures_lims_wh_samplesheet/000-Study.yml new file mode 100644 index 00000000..efefbef2 --- /dev/null +++ b/t/data/fixtures_lims_wh_samplesheet/000-Study.yml @@ -0,0 +1,363 @@ +--- +- abbreviation: 198STDY + abstract: ~ + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2008-11-13 13:27:48 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genotyping or cytogenetics + data_release_strategy: open + data_release_timing: standard + deleted_at: ~ + description: None + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: None + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 198 + id_study_tmp: 177 + last_updated: 2021-10-15 08:54:34 + name: Illumina Controls + prelim_id: ~ + recorded_at: 2021-10-15 08:54:35 + reference_genome: ' ' + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: ~ + study_type: Resequencing + study_visibility: Hold + uuid_study_lims: 2aa1cd2e-a557-11df-8092-00144f01a414 +- abbreviation: 521STDY + abstract: Transcriptome sequencing of Strongyloides ratti + accession_number: ERP001672 + aligned: 1 + array_express_accession_number: E-ERAD-92 + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2010-04-06 16:05:29 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: transcriptomics + data_release_strategy: open + data_release_timing: standard + deleted_at: ~ + description: "Strongyloides ratti is a common gastro-intestinal parasite of the rat." + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: Matthew + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 521 + id_study_tmp: 496 + last_updated: 2021-10-15 08:54:39 + name: Strongyloides ratti transcriptomics + prelim_id: ~ + recorded_at: 2021-10-15 08:54:42 + reference_genome: ' ' + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Transcriptome sequencing of Strongyloides ratti + study_type: Transcriptome Analysis + study_visibility: Hold + uuid_study_lims: 2d6848da-a557-11df-8092-00144f01a414 +- abbreviation: 700STDY + abstract: "Purpose of experiment" + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2010-10-07 15:11:00 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genomic sequencing + data_release_strategy: not applicable + data_release_timing: never + deleted_at: ~ + description: "I have agreed to alpha test the kapa hifi qPCR kit." + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: 0 + ethically_approved: ~ + faculty_sponsor: Harold + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 700 + id_study_tmp: 675 + last_updated: 2021-10-15 08:54:42 + name: Kapa HiFi test + prelim_id: ~ + recorded_at: 2021-10-15 08:54:47 + reference_genome: ' ' + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: hifi test + study_type: Whole Genome Sequencing + study_visibility: Hold + uuid_study_lims: e5f58d0c-d66e-11df-98a7-00144f206e2e +- abbreviation: 1697STDY + abstract: 'Identification of ivermectin resistance-conferring loci by sequencing and comparing the genomes of susceptible parents, resistant parents and backcross strains.' + accession_number: ERP000430 + aligned: 0 + array_express_accession_number: ~ + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2010-12-07 15:59:16 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genomic sequencing + data_release_strategy: open + data_release_timing: standard + deleted_at: ~ + description: Two H. contortus ivermectin resistance strains have been backcrossed. + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: Matthew Berriman + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 1697 + id_study_tmp: 1671 + last_updated: 2021-10-15 08:54:57 + name: Haemonchus contortus Ivermectin Resistance + prelim_id: ~ + recorded_at: 2021-10-15 08:55:05 + reference_genome: ' ' + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Haemonchus contortus Ivermectin Resistance + study_type: Whole Genome Sequencing + study_visibility: Hold + uuid_study_lims: 1b37a392-021b-11e0-9fca-00144f01a414 +- abbreviation: MPRandD + abstract: To establish a robust Mate Pair library preparation protocol + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2011-09-23 09:50:04 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genomic sequencing + data_release_strategy: not applicable + data_release_timing: never + deleted_at: ~ + description: R&D + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: 0 + ethically_approved: ~ + faculty_sponsor: Harold + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 1980 + id_study_tmp: 1954 + last_updated: 2021-10-15 08:55:04 + name: Mate Pair R&D + prelim_id: ~ + recorded_at: 2021-10-15 08:55:12 + reference_genome: Homo_sapiens (GRCh38_15) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Mate Pair R&D + study_type: Whole Genome Sequencing + study_visibility: Hold + uuid_study_lims: 69e77f84-e5c9-11e0-8713-68b59976a382 +- abbreviation: 2239STDY + abstract: 'Cancer is driven by mutation' + accession_number: EGAS00001000290 + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 1 + contaminated_human_dna: 0 + created: 2012-06-08 10:15:39 + data_access_group: cancer + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genomic sequencing + data_release_strategy: managed + data_release_timing: standard + deleted_at: ~ + description: 'Wholegenome libraries will be prepared.' + ega_dac_accession_number: EGAC00001000010 + ega_policy_accession_number: EGAP00001000037 + ena_project_id: PRJEB12 + ethically_approved: 1 + faculty_sponsor: Peter + hmdmc_number: 10/050 + id_lims: SQSCP + id_study_lims: 2239 + id_study_tmp: 2208 + last_updated: 2021-10-15 08:55:10 + name: MPN Whole Genomes + prelim_id: ~ + recorded_at: 2021-10-15 08:55:20 + reference_genome: Homo_sapiens (CGP_GRCh37.NCBI.allchr_MT) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: Myeloproliferative Disease Whole Genomes + study_type: Cancer Genomics + study_visibility: Hold + uuid_study_lims: e5bfd278-b152-11e1-b267-68b59976a382 +- abbreviation: 2501STDY + abstract: "Epigenetic mechanisms including non-coding RNAs" + accession_number: ERP002223 + aligned: 1 + array_express_accession_number: E-ERAD-155 + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2013-01-16 13:54:59 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: transcriptomics + data_release_strategy: not applicable + data_release_timing: never + deleted_at: ~ + description: "In order to examine the impact of genetic variation on epigenetic marking and control of gene expression." + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: David + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 2501 + id_study_tmp: 2470 + last_updated: 2021-10-15 08:55:16 + name: Mouse model to quantify genotype-epigenotype variations_RNA + prelim_id: ~ + recorded_at: 2021-10-15 08:55:27 + reference_genome: Mus_musculus (GRCm38) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: 'Mouse model to quantify genotype-epigenotype variations ' + study_type: Transcriptome Analysis + study_visibility: Public + uuid_study_lims: 516ac470-5fe4-11e2-9109-68b59976a382 +- abbreviation: 2658STDY + abstract: "This study aims to investigate." + accession_number: ERP003293 + aligned: 1 + array_express_accession_number: E-ERAD-186 + contains_human_dna: 0 + contaminated_human_dna: 0 + created: 2013-06-06 20:47:20 + data_access_group: ~ + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: transcriptomics + data_release_strategy: open + data_release_timing: standard + deleted_at: ~ + description: "This study aims to investigate\r\n" + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: ~ + faculty_sponsor: Sarah Teichmann + hmdmc_number: ~ + id_lims: SQSCP + id_study_lims: 2658 + id_study_tmp: 2627 + last_updated: 2021-10-15 08:55:20 + name: Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency + prelim_id: ~ + recorded_at: 2021-10-15 08:55:32 + reference_genome: Mus_musculus (NCBIm37) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: 'Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ' + study_type: Transcriptome Analysis + study_visibility: Hold + uuid_study_lims: 48187e10-ceea-11e2-941e-68b59976a382 + +- abbreviation: 6133STDY + abstract: 'Aim to determine age at acquisition of clonal haematopoiesis mutations, clonal architecture, and dynamics of clonal expansions.' + accession_number: ~ + aligned: 1 + array_express_accession_number: ~ + contains_human_dna: 1 + contaminated_human_dna: 0 + created: 2020-02-12 11:42:56 + data_access_group: cancer + data_deletion_period: ~ + data_destination: ~ + data_release_delay_period: ~ + data_release_delay_reason: ~ + data_release_sort_of_study: genomic sequencing + data_release_strategy: managed + data_release_timing: standard + deleted_at: ~ + description: Sequencing of blood stem cell-derived colonies. + ega_dac_accession_number: ~ + ega_policy_accession_number: ~ + ena_project_id: ~ + ethically_approved: 1 + faculty_sponsor: George + hmdmc_number: 17/006 + id_lims: SQSCP + id_study_lims: 6133 + id_study_tmp: 5963 + last_updated: 2021-10-15 08:56:39 + name: ImmunoAgeing_Colonies_WGS + prelim_id: ~ + recorded_at: 2021-10-15 08:57:06 + reference_genome: Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome) + remove_x_and_autosomes: 0 + s3_email_list: ~ + separate_y_chromosome_data: 0 + state: active + study_title: ImmunoAgeing_Colonies_WGS + study_type: Cancer Genomics + study_visibility: Hold + uuid_study_lims: d0099f20-4d8c-11ea-90fc-fa163e2f1184 + diff --git a/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml b/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml new file mode 100644 index 00000000..3313f624 --- /dev/null +++ b/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml @@ -0,0 +1,7054 @@ +--- +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019884 + id_library_lims: NT262278V + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271610 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789278 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:46 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 1 + tag_index: 1 + tag_sequence: ATCACGTT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019885 + id_library_lims: NT262279W + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271611 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789279 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 2 + tag_index: 2 + tag_sequence: CGATGTTT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019886 + id_library_lims: NT262280P + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271612 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789280 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 3 + tag_index: 3 + tag_sequence: TTAGGCAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019887 + id_library_lims: NT262281Q + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271613 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789281 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 4 + tag_index: 4 + tag_sequence: TGACCACT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019888 + id_library_lims: NT262282R + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271614 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789282 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 5 + tag_index: 5 + tag_sequence: ACAGTGGT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019889 + id_library_lims: NT262283S + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271615 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789283 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 6 + tag_index: 6 + tag_sequence: GCCAATGT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019890 + id_library_lims: NT262284T + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271616 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789284 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 7 + tag_index: 7 + tag_sequence: CAGATCTG + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019891 + id_library_lims: NT262285U + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271617 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 8 + tag_index: 8 + tag_sequence: ACTTGATG + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019892 + id_library_lims: NT262286V + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271618 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789286 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 9 + tag_index: 9 + tag_sequence: GATCAGCG + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019893 + id_library_lims: NT262287W + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271619 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789287 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 10 + tag_index: 10 + tag_sequence: TAGCTTGT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019894 + id_library_lims: NT262288A + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271620 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789288 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 11 + tag_index: 11 + tag_sequence: GGCTACAG + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 3789299 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0001310-300 + forward_read_length: 150 + id_flowcell_lims: 13994 + id_iseq_flowcell_tmp: 3019895 + id_library_lims: NT262289B + id_lims: SQSCP + id_pool_lims: NT262290R + id_sample_tmp: 1271621 + id_study_tmp: 675 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:36:43 + legacy_library_id: 3789289 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:36:47 + requested_insert_size_from: 200 + requested_insert_size_to: 700 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 12 + tag_index: 12 + tag_sequence: CTTGTACT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0702 + entity_id_lims: 3911772 + entity_type: library + external_release: 1 + flowcell_barcode: MS0001309-300 + forward_read_length: 150 + id_flowcell_lims: 14505 + id_iseq_flowcell_tmp: 3019896 + id_library_lims: NT262277U + id_lims: SQSCP + id_pool_lims: NT262277U + id_sample_tmp: 1271608 + id_study_tmp: 496 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2016-02-09 09:39:08 + legacy_library_id: 3789277 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:39:08 + requested_insert_size_from: 300 + requested_insert_size_to: 400 + reverse_read_length: 150 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + 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~ + tag2_set_name: ~ + tag_identifier: 1 + tag_index: 1 + tag_sequence: ATCACGTTAT + tag_set_id_lims: 7 + tag_set_name: '1 to 24 - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 4895948 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0009261-300 + forward_read_length: 130 + id_flowcell_lims: 16537 + id_iseq_flowcell_tmp: 3020610 + id_library_lims: NT283586V + id_lims: SQSCP + id_pool_lims: NT283588A + id_sample_tmp: 1373520 + id_study_tmp: 1954 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:53:17 + legacy_library_id: 4894528 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Long range + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:53:17 + requested_insert_size_from: 2000 + requested_insert_size_to: 6000 + reverse_read_length: 130 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 2 + tag_index: 2 + tag_sequence: CGATGTTTAT + tag_set_id_lims: 7 + tag_set_name: '1 to 24 - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 4895948 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0009261-300 + forward_read_length: 130 + id_flowcell_lims: 16537 + id_iseq_flowcell_tmp: 3020611 + id_library_lims: NT283585U + id_lims: SQSCP + id_pool_lims: NT283588A + id_sample_tmp: 1373519 + id_study_tmp: 1954 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:53:17 + legacy_library_id: 4894527 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Long range + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:53:17 + requested_insert_size_from: 2000 + requested_insert_size_to: 6000 + reverse_read_length: 130 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 8 + tag_index: 8 + tag_sequence: ACTTGATGAT + tag_set_id_lims: 7 + tag_set_name: '1 to 24 - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 4895948 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0009261-300 + forward_read_length: 130 + id_flowcell_lims: 16537 + id_iseq_flowcell_tmp: 3020612 + id_library_lims: NT283583S + id_lims: SQSCP + id_pool_lims: NT283588A + id_sample_tmp: 1373517 + id_study_tmp: 1954 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:53:17 + legacy_library_id: 4894525 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Long range + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:53:17 + requested_insert_size_from: 2000 + requested_insert_size_to: 6000 + reverse_read_length: 130 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 9 + tag_index: 9 + tag_sequence: GATCAGCGAT + tag_set_id_lims: 7 + tag_set_name: '1 to 24 - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0696 + entity_id_lims: 4895948 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: MS0009261-300 + forward_read_length: 130 + id_flowcell_lims: 16537 + id_iseq_flowcell_tmp: 3020613 + id_library_lims: NT283584T + id_lims: SQSCP + id_pool_lims: NT283588A + id_sample_tmp: 1373518 + id_study_tmp: 1954 + is_r_and_d: 1 + is_spiked: 0 + last_updated: 2016-02-09 09:53:17 + legacy_library_id: 4894526 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Long range + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 09:53:17 + requested_insert_size_from: 2000 + requested_insert_size_to: 6000 + reverse_read_length: 130 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 10 + tag_index: 10 + tag_sequence: TAGCTTGTAT + tag_set_id_lims: 7 + tag_set_name: '1 to 24 - 10 mer tags' + team: ~ + workflow: ~ +- bait_name: ~ + cost_code: S0702 + entity_id_lims: 8381746 + entity_type: library + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852275 + id_library_lims: NT332136W + id_lims: SQSCP + id_pool_lims: NT332136W + id_sample_tmp: 1640967 + id_study_tmp: 1671 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 7809257 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: No PCR + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 400 + requested_insert_size_to: 550 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: ~ + tag_index: ~ + tag_sequence: ~ + tag_set_id_lims: ~ + tag_set_name: ~ + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 8381746 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852274 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT332136W + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 1 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0702 + entity_id_lims: 8381744 + entity_type: library + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852277 + id_library_lims: NT332137A + id_lims: SQSCP + id_pool_lims: NT332137A + id_sample_tmp: 1640968 + id_study_tmp: 1671 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 7809258 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: No PCR + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 400 + requested_insert_size_to: 550 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: ~ + tag_index: ~ + tag_sequence: ~ + tag_set_id_lims: ~ + tag_set_name: ~ + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 8381744 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852276 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT332137A + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 2 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0702 + entity_id_lims: 8381745 + entity_type: library + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852279 + id_library_lims: NT332137A + id_lims: SQSCP + id_pool_lims: NT332137A + id_sample_tmp: 1640968 + id_study_tmp: 1671 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 7809258 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: No PCR + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 400 + requested_insert_size_to: 550 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: ~ + tag_index: ~ + tag_sequence: ~ + tag_set_id_lims: ~ + tag_set_name: ~ + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 8381745 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852278 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT332137A + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 3 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852281 + id_library_lims: NT342271K + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685062 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215019 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 1 + tag_index: 1 + tag_sequence: TAAGGCGATAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852282 + id_library_lims: NT342272L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685063 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215020 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 2 + tag_index: 2 + tag_sequence: CGTACTAGTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852283 + id_library_lims: NT342273M + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685064 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215021 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 3 + tag_index: 3 + tag_sequence: AGGCAGAATAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852284 + id_library_lims: NT342274N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685065 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215022 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 4 + tag_index: 4 + tag_sequence: TCCTGAGCTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852285 + id_library_lims: NT342275O + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685066 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215023 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 5 + tag_index: 5 + tag_sequence: GGACTCCTTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852286 + id_library_lims: NT342276P + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685067 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215024 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 6 + tag_index: 6 + tag_sequence: TAGGCATGTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852287 + id_library_lims: NT342277Q + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685068 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215025 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 7 + tag_index: 7 + tag_sequence: CTCTCTACTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852288 + id_library_lims: NT342278R + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685069 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215026 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 8 + tag_index: 8 + tag_sequence: CAGAGAGGTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852289 + id_library_lims: NT342279S + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685070 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215027 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 9 + tag_index: 9 + tag_sequence: GCTACGCTTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852290 + id_library_lims: NT342280L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685071 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215028 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 10 + tag_index: 10 + tag_sequence: CGAGGCTGTAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852291 + id_library_lims: NT342281M + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685072 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215029 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 11 + tag_index: 11 + tag_sequence: AAGAGGCATAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852292 + id_library_lims: NT342282N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685073 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215030 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 12 + tag_index: 12 + tag_sequence: GTAGAGGATAGATCGC + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852293 + id_library_lims: NT342283O + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685074 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215031 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 13 + tag_index: 13 + tag_sequence: TAAGGCGACTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852294 + id_library_lims: NT342284P + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685075 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215032 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 14 + tag_index: 14 + tag_sequence: CGTACTAGCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852295 + id_library_lims: NT342285Q + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685076 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215033 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 15 + tag_index: 15 + tag_sequence: AGGCAGAACTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852296 + id_library_lims: NT342286R + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685077 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215034 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 16 + tag_index: 16 + tag_sequence: TCCTGAGCCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852297 + id_library_lims: NT342287S + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685078 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215035 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 17 + tag_index: 17 + tag_sequence: GGACTCCTCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852298 + id_library_lims: NT342288T + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685079 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215036 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 18 + tag_index: 18 + tag_sequence: TAGGCATGCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852299 + id_library_lims: NT342289U + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685080 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215037 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 19 + tag_index: 19 + tag_sequence: CTCTCTACCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852300 + id_library_lims: NT342290N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685081 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215038 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 20 + tag_index: 20 + tag_sequence: CAGAGAGGCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852301 + id_library_lims: NT342291O + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685082 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215039 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 21 + tag_index: 21 + tag_sequence: GCTACGCTCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852302 + id_library_lims: NT342292P + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685083 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215040 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 22 + tag_index: 22 + tag_sequence: CGAGGCTGCTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852303 + id_library_lims: NT342293Q + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685084 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215041 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 23 + tag_index: 23 + tag_sequence: AAGAGGCACTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852304 + id_library_lims: NT342294R + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685085 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215042 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 24 + tag_index: 24 + tag_sequence: GTAGAGGACTCTCTAT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852305 + id_library_lims: NT342295S + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685086 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215043 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 25 + tag_index: 25 + tag_sequence: TAAGGCGATATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852306 + id_library_lims: NT342296T + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685087 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215044 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 26 + tag_index: 26 + tag_sequence: CGTACTAGTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852307 + id_library_lims: NT342297U + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685088 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215045 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 27 + tag_index: 27 + tag_sequence: AGGCAGAATATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852308 + id_library_lims: NT342298V + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685089 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215046 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 28 + tag_index: 28 + tag_sequence: TCCTGAGCTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852309 + id_library_lims: NT342299W + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685090 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215047 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 29 + tag_index: 29 + tag_sequence: GGACTCCTTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852310 + id_library_lims: NT342300V + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685091 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215048 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 30 + tag_index: 30 + tag_sequence: TAGGCATGTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852311 + id_library_lims: NT342301W + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685092 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215049 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 31 + tag_index: 31 + tag_sequence: CTCTCTACTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852312 + id_library_lims: NT342302A + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685093 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215050 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 32 + tag_index: 32 + tag_sequence: CAGAGAGGTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852313 + id_library_lims: NT342303B + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685094 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215051 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 33 + tag_index: 33 + tag_sequence: GCTACGCTTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852314 + id_library_lims: NT342304C + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685095 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215052 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 34 + tag_index: 34 + tag_sequence: CGAGGCTGTATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852315 + id_library_lims: NT342305D + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685096 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215053 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 35 + tag_index: 35 + tag_sequence: AAGAGGCATATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852316 + id_library_lims: NT342306E + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685097 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215054 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 36 + tag_index: 36 + tag_sequence: GTAGAGGATATCCTCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852317 + id_library_lims: NT342307F + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685098 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215055 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 37 + tag_index: 37 + tag_sequence: TAAGGCGAAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852318 + id_library_lims: NT342308G + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685099 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215056 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 38 + tag_index: 38 + tag_sequence: CGTACTAGAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852319 + id_library_lims: NT342309H + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685100 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215057 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 39 + tag_index: 39 + tag_sequence: AGGCAGAAAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852320 + id_library_lims: NT342310A + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685101 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215058 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 40 + tag_index: 40 + tag_sequence: TCCTGAGCAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852321 + id_library_lims: NT342311B + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685102 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215059 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 41 + tag_index: 41 + tag_sequence: GGACTCCTAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852322 + id_library_lims: NT342312C + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685103 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215060 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 42 + tag_index: 42 + tag_sequence: TAGGCATGAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852323 + id_library_lims: NT342313D + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685104 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215061 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 43 + tag_index: 43 + tag_sequence: CTCTCTACAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852324 + id_library_lims: NT342314E + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685105 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215062 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 44 + tag_index: 44 + tag_sequence: CAGAGAGGAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852325 + id_library_lims: NT342315F + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685106 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215063 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 45 + tag_index: 45 + tag_sequence: GCTACGCTAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852326 + id_library_lims: NT342316G + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685107 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215064 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 46 + tag_index: 46 + tag_sequence: CGAGGCTGAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852327 + id_library_lims: NT342317H + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685108 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215065 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 47 + tag_index: 47 + tag_sequence: AAGAGGCAAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852328 + id_library_lims: NT342318I + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685109 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215066 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 48 + tag_index: 48 + tag_sequence: GTAGAGGAAGAGTAGA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852329 + id_library_lims: NT342319J + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685110 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215067 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 49 + tag_index: 49 + tag_sequence: TAAGGCGAGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852330 + id_library_lims: NT342320C + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685111 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215068 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 50 + tag_index: 50 + tag_sequence: CGTACTAGGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852331 + id_library_lims: NT342321D + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685112 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215069 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 51 + tag_index: 51 + tag_sequence: AGGCAGAAGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852332 + id_library_lims: NT342322E + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685113 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215070 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 52 + tag_index: 52 + tag_sequence: TCCTGAGCGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852333 + id_library_lims: NT342323F + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685114 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215071 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 53 + tag_index: 53 + tag_sequence: GGACTCCTGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852334 + id_library_lims: NT342324G + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685115 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215072 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 54 + tag_index: 54 + tag_sequence: TAGGCATGGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852335 + id_library_lims: NT342325H + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685116 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215073 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 55 + tag_index: 55 + tag_sequence: CTCTCTACGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852336 + id_library_lims: NT342326I + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685117 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215074 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 56 + tag_index: 56 + tag_sequence: CAGAGAGGGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852337 + id_library_lims: NT342327J + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685118 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215075 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 57 + tag_index: 57 + tag_sequence: GCTACGCTGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852338 + id_library_lims: NT342328K + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685119 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215076 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 58 + tag_index: 58 + tag_sequence: CGAGGCTGGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852339 + id_library_lims: NT342329L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685120 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215077 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 59 + tag_index: 59 + tag_sequence: AAGAGGCAGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852340 + id_library_lims: NT342330E + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685121 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215078 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 60 + tag_index: 60 + tag_sequence: GTAGAGGAGTAAGGAG + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852341 + id_library_lims: NT342331F + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685122 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215079 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 61 + tag_index: 61 + tag_sequence: TAAGGCGAACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852342 + id_library_lims: NT342332G + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685123 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215080 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 62 + tag_index: 62 + tag_sequence: CGTACTAGACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852343 + id_library_lims: NT342333H + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685124 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215081 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 63 + tag_index: 63 + tag_sequence: AGGCAGAAACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852344 + id_library_lims: NT342334I + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685125 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215082 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 64 + tag_index: 64 + tag_sequence: TCCTGAGCACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852345 + id_library_lims: NT342335J + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685126 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215083 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 65 + tag_index: 65 + tag_sequence: GGACTCCTACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852346 + id_library_lims: NT342336K + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685127 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215084 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 66 + tag_index: 66 + tag_sequence: TAGGCATGACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852347 + id_library_lims: NT342337L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685128 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215085 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 67 + tag_index: 67 + tag_sequence: CTCTCTACACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852348 + id_library_lims: NT342338M + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685129 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215086 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 68 + tag_index: 68 + tag_sequence: CAGAGAGGACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852349 + id_library_lims: NT342339N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685130 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215087 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 69 + tag_index: 69 + tag_sequence: GCTACGCTACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852350 + id_library_lims: NT342340G + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685131 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215088 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 70 + tag_index: 70 + tag_sequence: CGAGGCTGACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852351 + id_library_lims: NT342341H + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685132 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215089 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 71 + tag_index: 71 + tag_sequence: AAGAGGCAACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852352 + id_library_lims: NT342342I + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685133 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215090 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 72 + tag_index: 72 + tag_sequence: GTAGAGGAACTGCATA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852353 + id_library_lims: NT342343J + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685134 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215091 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 73 + tag_index: 73 + tag_sequence: TAAGGCGAAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852354 + id_library_lims: NT342344K + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685135 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215092 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 74 + tag_index: 74 + tag_sequence: CGTACTAGAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852355 + id_library_lims: NT342345L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685136 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215093 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 75 + tag_index: 75 + tag_sequence: AGGCAGAAAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852356 + id_library_lims: NT342346M + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685137 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215094 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 76 + tag_index: 76 + tag_sequence: TCCTGAGCAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852357 + id_library_lims: NT342347N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685138 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215095 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 77 + tag_index: 77 + tag_sequence: GGACTCCTAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852358 + id_library_lims: NT342348O + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685139 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215096 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 78 + tag_index: 78 + tag_sequence: TAGGCATGAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852359 + id_library_lims: NT342349P + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685140 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215097 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 79 + tag_index: 79 + tag_sequence: CTCTCTACAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852360 + id_library_lims: NT342350I + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685141 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215098 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 80 + tag_index: 80 + tag_sequence: CAGAGAGGAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852361 + id_library_lims: NT342351J + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685142 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215099 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 81 + tag_index: 81 + tag_sequence: GCTACGCTAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852362 + id_library_lims: NT342352K + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685143 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215100 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 82 + tag_index: 82 + tag_sequence: CGAGGCTGAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852363 + id_library_lims: NT342353L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685144 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215101 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 83 + tag_index: 83 + tag_sequence: AAGAGGCAAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852364 + id_library_lims: NT342354M + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685145 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215102 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 84 + tag_index: 84 + tag_sequence: GTAGAGGAAAGGAGTA + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852365 + id_library_lims: NT342355N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685146 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215103 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 85 + tag_index: 85 + tag_sequence: TAAGGCGACTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852366 + id_library_lims: NT342356O + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685147 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215104 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 86 + tag_index: 86 + tag_sequence: CGTACTAGCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852367 + id_library_lims: NT342357P + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685148 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215105 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 87 + tag_index: 87 + tag_sequence: AGGCAGAACTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852368 + id_library_lims: NT342358Q + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685149 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215106 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 88 + tag_index: 88 + tag_sequence: TCCTGAGCCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852369 + id_library_lims: NT342359R + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685150 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215107 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 89 + tag_index: 89 + tag_sequence: GGACTCCTCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852370 + id_library_lims: NT342360K + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685151 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215108 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 90 + tag_index: 90 + tag_sequence: TAGGCATGCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852371 + id_library_lims: NT342361L + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685152 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215109 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 91 + tag_index: 91 + tag_sequence: CTCTCTACCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852372 + id_library_lims: NT342362M + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685153 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215110 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 92 + tag_index: 92 + tag_sequence: CAGAGAGGCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852373 + id_library_lims: NT342363N + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685154 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215111 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 93 + tag_index: 93 + tag_sequence: GCTACGCTCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852374 + id_library_lims: NT342364O + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685155 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215112 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 94 + tag_index: 94 + tag_sequence: CGAGGCTGCTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852375 + id_library_lims: NT342365P + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685156 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215113 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 95 + tag_index: 95 + tag_sequence: AAGAGGCACTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0917 + entity_id_lims: 8381739 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852376 + id_library_lims: NT342366Q + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1685157 + id_study_tmp: 2627 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8215114 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: qPCR only + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 96 + tag_index: 96 + tag_sequence: GTAGAGGACTAAGCCT + tag_set_id_lims: 24 + tag_set_name: 'Nextera DUAL v2 - 96 tags - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 8381739 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852280 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT342446P + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 4 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:19 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S0814 + entity_id_lims: 8381740 + entity_type: library + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852378 + id_library_lims: NT342910S + id_lims: SQSCP + id_pool_lims: NT342910S + id_sample_tmp: 1690652 + id_study_tmp: 2208 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8269740 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: No PCR + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 300 + requested_insert_size_to: 500 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: ~ + tag_index: ~ + tag_sequence: ~ + tag_set_id_lims: ~ + tag_set_name: ~ + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 8381740 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852377 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT342910S + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 5 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S1553 + entity_id_lims: 8381741 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852380 + id_library_lims: NT343420J + id_lims: SQSCP + id_pool_lims: NT343441O + id_sample_tmp: 1673167 + id_study_tmp: 2470 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8324592 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Pre-quality controlled + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 100 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 64 + tag_index: 64 + tag_sequence: GAGATTCCTAATCTTA + tag_set_id_lims: 37 + tag_set_name: 'Illumina_dual_indexed96 - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S1553 + entity_id_lims: 8381741 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852381 + id_library_lims: NT343421K + id_lims: SQSCP + id_pool_lims: NT343441O + id_sample_tmp: 1673168 + id_study_tmp: 2470 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8324593 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Pre-quality controlled + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 100 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 65 + tag_index: 65 + tag_sequence: ATTCAGAATAATCTTA + tag_set_id_lims: 37 + tag_set_name: 'Illumina_dual_indexed96 - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: ~ + entity_id_lims: 8381741 + entity_type: library_indexed_spike + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852379 + id_library_lims: NT310838E + id_lims: SQSCP + id_pool_lims: NT343441O + id_sample_tmp: 1237247 + id_study_tmp: 177 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 6 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S1553 + entity_id_lims: 8381742 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852383 + id_library_lims: NT343422L + id_lims: SQSCP + id_pool_lims: NT343442P + id_sample_tmp: 1673169 + id_study_tmp: 2470 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8324594 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Pre-quality controlled + position: 7 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 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primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S1553 + entity_id_lims: 8381743 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852386 + id_library_lims: NT343424N + id_lims: SQSCP + id_pool_lims: NT343444R + id_sample_tmp: 1673171 + id_study_tmp: 2470 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8324596 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: Pre-quality controlled + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: 100 + requested_insert_size_to: 1000 + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 88 + tag_index: 88 + tag_sequence: GAGATTCCGTACTGAC + tag_set_id_lims: 37 + tag_set_name: 'Illumina_dual_indexed96 - 16mer' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S1553 + entity_id_lims: 8381743 + entity_type: library_indexed + external_release: 1 + flowcell_barcode: C2M2HACXX + forward_read_length: 100 + id_flowcell_lims: 23798 + id_iseq_flowcell_tmp: 2852387 + id_library_lims: NT343425O + id_lims: SQSCP + id_pool_lims: NT343444R + id_sample_tmp: 1673172 + id_study_tmp: 2470 + is_r_and_d: 0 + is_spiked: 1 + last_updated: 2016-02-09 11:12:09 + legacy_library_id: 8324597 + 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2016-02-09 11:12:09 + legacy_library_id: 6200285 + loading_concentration: ~ + manual_qc: 1 + pipeline_id_lims: ~ + position: 8 + primer_panel: ~ + priority: 0 + purpose: standard + recorded_at: 2016-02-09 11:12:20 + requested_insert_size_from: ~ + requested_insert_size_to: ~ + reverse_read_length: 100 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: ~ + tag2_identifier: ~ + tag2_sequence: ~ + tag2_set_id_lims: ~ + tag2_set_name: ~ + tag_identifier: 168 + tag_index: 168 + tag_sequence: ACAACGCAAT + tag_set_id_lims: 6 + tag_set_name: 'Sanger_168tags - 10 mer tags' + team: Illumina-C + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542489 + id_library_lims: DN589410K:C1 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339231 + id_study_tmp: 5963 + is_r_and_d: 0 + 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4339234 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2020-08-10 21:00:48 + legacy_library_id: 27037100 + loading_concentration: ~ + manual_qc: 0 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 6 + tag2_sequence: CTCCATAA + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 6 + tag_index: 2 + tag_sequence: ACTTAGAG + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542491 + id_library_lims: DN589410K:G1 + id_lims: 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~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 50 + tag2_sequence: ACTTCCGA + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 50 + tag_index: 16 + tag_sequence: TGATTTCC + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542505 + id_library_lims: DN589410K:E7 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339281 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2020-08-10 21:00:48 + legacy_library_id: 27037094 + loading_concentration: ~ + manual_qc: 0 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 53 + tag2_sequence: ACGTTTAA + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 53 + tag_index: 17 + tag_sequence: TTTAAATG + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542506 + id_library_lims: DN589410K:F7 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339282 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2020-08-10 21:00:48 + legacy_library_id: 27037106 + loading_concentration: ~ + manual_qc: 0 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 54 + tag2_sequence: ACGCCGCG + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 54 + tag_index: 18 + tag_sequence: ACCTGCGG + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542507 + id_library_lims: DN589410K:A8 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339285 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + 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~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542514 + id_library_lims: DN589410K:B10 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339302 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2020-08-10 21:00:48 + legacy_library_id: 27037061 + loading_concentration: ~ + manual_qc: 0 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 74 + tag2_sequence: AAGCTCCG + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 74 + tag_index: 26 + tag_sequence: CTCTTTAT + tag_set_id_lims: 191 + tag_set_name: 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spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 85 + tag2_sequence: GAAGAGCC + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 85 + tag_index: 30 + tag_sequence: CTCGACGT + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542519 + id_library_lims: DN589410K:F11 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339314 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2020-08-10 21:00:48 + legacy_library_id: 27037110 + loading_concentration: ~ + manual_qc: 0 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 86 + tag2_sequence: ATCCTGAG + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 86 + tag_index: 31 + tag_sequence: AGTTGCAA + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ +- bait_name: ~ + cost_code: S4360 + entity_id_lims: 30355804 + entity_type: library_indexed + external_release: 0 + flowcell_barcode: MS9462968-50V2 + forward_read_length: 25 + id_flowcell_lims: 76873 + id_iseq_flowcell_tmp: 7542520 + id_library_lims: DN589410K:A12 + id_lims: SQSCP + id_pool_lims: NT1625362I + id_sample_tmp: 4339317 + id_study_tmp: 5963 + is_r_and_d: 0 + is_spiked: 0 + last_updated: 2020-08-10 21:00:48 + legacy_library_id: 27037051 + loading_concentration: ~ + manual_qc: 0 + pipeline_id_lims: Standard + position: 1 + primer_panel: ~ + priority: 3 + purpose: standard + recorded_at: 2020-08-10 21:00:49 + requested_insert_size_from: 450 + requested_insert_size_to: 450 + reverse_read_length: 25 + spiked_phix_barcode: ~ + spiked_phix_percentage: ~ + suboptimal: 1 + tag2_identifier: 89 + tag2_sequence: AAAGGCTG + tag2_set_id_lims: 190 + tag2_set_name: TS_RNAhWGS_UDI96_i5 + tag_identifier: 89 + tag_index: 32 + tag_sequence: GTAAGATG + tag_set_id_lims: 191 + tag_set_name: TS_RNAhWGS_UDI96_i7 + team: Illumina-HTP + workflow: ~ + diff --git a/t/data/fixtures_lims_wh_samplesheet/100-StudyUser.yml b/t/data/fixtures_lims_wh_samplesheet/100-StudyUser.yml new file mode 100644 index 00000000..1493987f --- /dev/null +++ b/t/data/fixtures_lims_wh_samplesheet/100-StudyUser.yml @@ -0,0 +1,37 @@ +--- +- email: user1@sanger.ac.uk + id_study_tmp: 5963 + id_study_users_tmp: 530314 + last_updated: 2021-10-15 08:56:39 + login: user1 + name: Claire + role: manager +- email: user2@sanger.ac.uk + id_study_tmp: 5963 + id_study_users_tmp: 530316 + last_updated: 2021-10-15 08:56:39 + login: user2 + name: Calli + role: manager +- email: user3@sanger.ac.uk + id_study_tmp: 5963 + id_study_users_tmp: 530318 + last_updated: 2021-10-15 08:56:39 + login: user3 + name: Laura + role: manager +- email: user1@sanger.ac.uk + id_study_tmp: 5963 + id_study_users_tmp: 530320 + last_updated: 2021-10-15 08:56:39 + login: user1 + name: Claire + role: owner +- email: user4@sanger.ac.uk + id_study_tmp: 5963 + id_study_users_tmp: 530322 + last_updated: 2021-10-15 08:56:39 + login: user4 + name: Margarete + role: follower + diff --git a/t/data/samplesheet/1control7libs_extended.csv b/t/data/samplesheet/1control7libs_extended.csv deleted file mode 100644 index 164acddc..00000000 --- a/t/data/samplesheet/1control7libs_extended.csv +++ /dev/null @@ -1,10 +0,0 @@ -[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -Lane,Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -1,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36189,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, -2,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36199,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, -3,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36202,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, -4,79577,phiX CT1462-2 1,,,,,,,,,,,1,0,,,phiX CT1462-2 1,,,,,,standard,,43779,,,,,,,,,9836,,phiX CT1462-2 1,,,,,,,0,0,,,,,,,, -5,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36203,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, -6,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36209,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, -7,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36210,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, -8,57440,EGAN00001001569,,,,,,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk,dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk,sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,,,PD3918a 1,Human,9606,S0277,333,CLL whole genome,standard,pass,36211,from:300 to:400,EGAN00001001569,,Homo sapiens,,,,,7283,,PD3918a,,,,,EGAS00001000014,1,0,0,Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information%2C and the identification of novel rearranged cancer genes and gene fusions.,333,CLL whole genome,,,CLL Cancer Whole Genome Sequencing,, diff --git a/t/data/samplesheet/4pool4libs_extended.csv b/t/data/samplesheet/4pool4libs_extended.csv index 344ab8b1..d3d3d0d3 100644 --- a/t/data/samplesheet/4pool4libs_extended.csv +++ b/t/data/samplesheet/4pool4libs_extended.csv @@ -1,112 +1,112 @@ [Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -1,7809257,ERS323818,,,,,No PCR,,,hr1@sanger.ac.uk jc17@sanger.ac.uk neh@sanger.ac.uk,jc17@sanger.ac.uk neh@sanger.ac.uk,neh@sanger.ac.uk,hr1@sanger.ac.uk,,0,0,8381746,0,Hc_4_BC4_P2_5046_340285 7809257,Haemonchus contortus,6289,S0702,714,Haemonchus contortus Ivermectin Resistance Genomics Study,standard,,5707613,from:400 to:550,ERS323818,,Haemonchus contortus,,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660679,,Hc_4_BC4_P2_5046_340285,Haemonchus contortus MHco3%2F4.BC4(P2)-5046,Haemonchus_contortus (V1_21June13),,168,ERP000430,,0,0,Two H. contortus ivermectin resistance strains have been backcrossed 4 times against the susceptible genome strain. Parental strains and backcross strains will be sequenced in order to identify regions of the genome linked to ivermectin resistance-conferring loci.,1697,Haemonchus contortus Ivermectin Resistance,,,Haemonchus contortus Ivermectin Resistance,, -2,7809258,ERS323819,,,,,No PCR,,,hr1@sanger.ac.uk jc17@sanger.ac.uk neh@sanger.ac.uk,jc17@sanger.ac.uk neh@sanger.ac.uk,neh@sanger.ac.uk,hr1@sanger.ac.uk,,0,0,8381744,0,Hc_10_BC4_P2_5779_340285 7809258,Haemonchus contortus,6289,S0702,714,Haemonchus contortus Ivermectin Resistance Genomics Study,standard,,5707611,from:400 to:550,ERS323819,,Haemonchus contortus,,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,,0,0,Two H. contortus ivermectin resistance strains have been backcrossed 4 times against the susceptible genome strain. Parental strains and backcross strains will be sequenced in order to identify regions of the genome linked to ivermectin resistance-conferring loci.,1697,Haemonchus contortus Ivermectin Resistance,,,Haemonchus contortus Ivermectin Resistance,, -3,7809258,ERS323819,,,,,No PCR,,,hr1@sanger.ac.uk jc17@sanger.ac.uk neh@sanger.ac.uk,jc17@sanger.ac.uk neh@sanger.ac.uk,neh@sanger.ac.uk,hr1@sanger.ac.uk,,0,0,8381745,0,Hc_10_BC4_P2_5779_340285 7809258,Haemonchus contortus,6289,S0702,714,Haemonchus contortus Ivermectin Resistance Genomics Study,standard,,5707612,from:400 to:550,ERS323819,,Haemonchus contortus,,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,,0,0,Two H. contortus ivermectin resistance strains have been backcrossed 4 times against the susceptible genome strain. Parental strains and backcross strains will be sequenced in order to identify regions of the genome linked to ivermectin resistance-conferring loci.,1697,Haemonchus contortus Ivermectin Resistance,,,Haemonchus contortus Ivermectin Resistance,, -4,8215019,ERS351213,,TAAGGCGA,TAGATCGC,,qPCR only,TAAGGCGATAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell1 8215019,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351213,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706390,,mES_ai2_s2_cell1,mES_ai2_s2_cell1,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,1, -4,8215020,ERS351214,,CGTACTAG,TAGATCGC,,qPCR only,CGTACTAGTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell2 8215020,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351214,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706391,,mES_ai2_s2_cell2,mES_ai2_s2_cell2,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,2, -4,8215021,ERS351221,,AGGCAGAA,TAGATCGC,,qPCR only,AGGCAGAATAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell3 8215021,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351221,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706392,,mES_ai2_s2_cell3,mES_ai2_s2_cell3,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,3, -4,8215022,ERS351222,,TCCTGAGC,TAGATCGC,,qPCR only,TCCTGAGCTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell4 8215022,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351222,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706393,,mES_ai2_s2_cell4,mES_ai2_s2_cell4,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,4, -4,8215023,ERS351223,,GGACTCCT,TAGATCGC,,qPCR only,GGACTCCTTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell5 8215023,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351223,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706394,,mES_ai2_s2_cell5,mES_ai2_s2_cell5,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,5, -4,8215024,ERS351224,,TAGGCATG,TAGATCGC,,qPCR only,TAGGCATGTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell6 8215024,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351224,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706395,,mES_ai2_s2_cell6,mES_ai2_s2_cell6,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,6, -4,8215025,ERS351225,,CTCTCTAC,TAGATCGC,,qPCR only,CTCTCTACTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell7 8215025,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351225,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706396,,mES_ai2_s2_cell7,mES_ai2_s2_cell7,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,7, -4,8215026,ERS351218,,CAGAGAGG,TAGATCGC,,qPCR only,CAGAGAGGTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell8 8215026,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351218,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706397,,mES_ai2_s2_cell8,mES_ai2_s2_cell8,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,8, -4,8215027,ERS351219,,GCTACGCT,TAGATCGC,,qPCR only,GCTACGCTTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell9 8215027,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351219,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706398,,mES_ai2_s2_cell9,mES_ai2_s2_cell9,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,9, -4,8215028,ERS351220,,CGAGGCTG,TAGATCGC,,qPCR only,CGAGGCTGTAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell10 8215028,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351220,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706399,,mES_ai2_s2_cell10,mES_ai2_s2_cell10,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,10, -4,8215029,ERS351235,,AAGAGGCA,TAGATCGC,,qPCR only,AAGAGGCATAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell11 8215029,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351235,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706400,,mES_ai2_s2_cell11,mES_ai2_s2_cell11,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,11, -4,8215030,ERS351237,,GTAGAGGA,TAGATCGC,,qPCR only,GTAGAGGATAGATCGC,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell12 8215030,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351237,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706401,,mES_ai2_s2_cell12,mES_ai2_s2_cell12,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,12, -4,8215031,ERS351238,,TAAGGCGA,CTCTCTAT,,qPCR only,TAAGGCGACTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell13 8215031,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351238,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706402,,mES_ai2_s2_cell13,mES_ai2_s2_cell13,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,13, -4,8215032,ERS351239,,CGTACTAG,CTCTCTAT,,qPCR only,CGTACTAGCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell14 8215032,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351239,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706403,,mES_ai2_s2_cell14,mES_ai2_s2_cell14,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,14, -4,8215033,ERS351241,,AGGCAGAA,CTCTCTAT,,qPCR only,AGGCAGAACTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell15 8215033,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351241,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706404,,mES_ai2_s2_cell15,mES_ai2_s2_cell15,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,15, -4,8215034,ERS351226,,TCCTGAGC,CTCTCTAT,,qPCR only,TCCTGAGCCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell16 8215034,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351226,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706405,,mES_ai2_s2_cell16,mES_ai2_s2_cell16,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,16, -4,8215035,ERS351227,,GGACTCCT,CTCTCTAT,,qPCR only,GGACTCCTCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell17 8215035,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351227,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706406,,mES_ai2_s2_cell17,mES_ai2_s2_cell17,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,17, -4,8215036,ERS351234,,TAGGCATG,CTCTCTAT,,qPCR only,TAGGCATGCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell18 8215036,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351234,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706407,,mES_ai2_s2_cell18,mES_ai2_s2_cell18,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,18, -4,8215037,ERS351236,,CTCTCTAC,CTCTCTAT,,qPCR only,CTCTCTACCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell19 8215037,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351236,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706408,,mES_ai2_s2_cell19,mES_ai2_s2_cell19,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,19, -4,8215038,ERS351247,,CAGAGAGG,CTCTCTAT,,qPCR only,CAGAGAGGCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell20 8215038,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351247,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706409,,mES_ai2_s2_cell20,mES_ai2_s2_cell20,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,20, -4,8215039,ERS351249,,GCTACGCT,CTCTCTAT,,qPCR only,GCTACGCTCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell21 8215039,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351249,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706410,,mES_ai2_s2_cell21,mES_ai2_s2_cell21,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,21, -4,8215040,ERS351251,,CGAGGCTG,CTCTCTAT,,qPCR only,CGAGGCTGCTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell22 8215040,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351251,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706411,,mES_ai2_s2_cell22,mES_ai2_s2_cell22,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,22, -4,8215041,ERS351252,,AAGAGGCA,CTCTCTAT,,qPCR only,AAGAGGCACTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell23 8215041,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351252,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706412,,mES_ai2_s2_cell23,mES_ai2_s2_cell23,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,23, -4,8215042,ERS351242,,GTAGAGGA,CTCTCTAT,,qPCR only,GTAGAGGACTCTCTAT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell24 8215042,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351242,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706413,,mES_ai2_s2_cell24,mES_ai2_s2_cell24,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,24, -4,8215043,ERS351243,,TAAGGCGA,TATCCTCT,,qPCR only,TAAGGCGATATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell25 8215043,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351243,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706414,,mES_ai2_s2_cell25,mES_ai2_s2_cell25,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,25, -4,8215044,ERS351244,,CGTACTAG,TATCCTCT,,qPCR only,CGTACTAGTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell26 8215044,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351244,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706415,,mES_ai2_s2_cell26,mES_ai2_s2_cell26,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,26, -4,8215045,ERS351245,,AGGCAGAA,TATCCTCT,,qPCR only,AGGCAGAATATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell27 8215045,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351245,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706416,,mES_ai2_s2_cell27,mES_ai2_s2_cell27,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,27, -4,8215046,ERS351248,,TCCTGAGC,TATCCTCT,,qPCR only,TCCTGAGCTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell28 8215046,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351248,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706417,,mES_ai2_s2_cell28,mES_ai2_s2_cell28,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,28, -4,8215047,ERS351250,,GGACTCCT,TATCCTCT,,qPCR only,GGACTCCTTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell29 8215047,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351250,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706418,,mES_ai2_s2_cell29,mES_ai2_s2_cell29,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,29, -4,8215048,ERS351260,,TAGGCATG,TATCCTCT,,qPCR only,TAGGCATGTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell30 8215048,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351260,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706419,,mES_ai2_s2_cell30,mES_ai2_s2_cell30,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,30, -4,8215049,ERS351261,,CTCTCTAC,TATCCTCT,,qPCR only,CTCTCTACTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell31 8215049,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351261,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706420,,mES_ai2_s2_cell31,mES_ai2_s2_cell31,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,31, -4,8215050,ERS351254,,CAGAGAGG,TATCCTCT,,qPCR only,CAGAGAGGTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell32 8215050,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351254,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706421,,mES_ai2_s2_cell32,mES_ai2_s2_cell32,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,32, -4,8215051,ERS351255,,GCTACGCT,TATCCTCT,,qPCR only,GCTACGCTTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell33 8215051,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351255,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706422,,mES_ai2_s2_cell33,mES_ai2_s2_cell33,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,33, -4,8215052,ERS351256,,CGAGGCTG,TATCCTCT,,qPCR only,CGAGGCTGTATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell34 8215052,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351256,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706423,,mES_ai2_s2_cell34,mES_ai2_s2_cell34,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,34, -4,8215053,ERS351257,,AAGAGGCA,TATCCTCT,,qPCR only,AAGAGGCATATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell35 8215053,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351257,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706424,,mES_ai2_s2_cell35,mES_ai2_s2_cell35,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,35, -4,8215054,ERS351258,,GTAGAGGA,TATCCTCT,,qPCR only,GTAGAGGATATCCTCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell36 8215054,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351258,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706425,,mES_ai2_s2_cell36,mES_ai2_s2_cell36,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,36, -4,8215055,ERS351259,,TAAGGCGA,AGAGTAGA,,qPCR only,TAAGGCGAAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell37 8215055,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351259,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706426,,mES_ai2_s2_cell37,mES_ai2_s2_cell37,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,37, -4,8215056,ERS351269,,CGTACTAG,AGAGTAGA,,qPCR only,CGTACTAGAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell38 8215056,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351269,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706427,,mES_ai2_s2_cell38,mES_ai2_s2_cell38,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,38, -4,8215057,ERS351271,,AGGCAGAA,AGAGTAGA,,qPCR only,AGGCAGAAAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell39 8215057,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351271,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706428,,mES_ai2_s2_cell39,mES_ai2_s2_cell39,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,39, -4,8215058,ERS351262,,TCCTGAGC,AGAGTAGA,,qPCR only,TCCTGAGCAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell40 8215058,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351262,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706429,,mES_ai2_s2_cell40,mES_ai2_s2_cell40,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,40, -4,8215059,ERS351263,,GGACTCCT,AGAGTAGA,,qPCR only,GGACTCCTAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell41 8215059,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351263,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706430,,mES_ai2_s2_cell41,mES_ai2_s2_cell41,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,41, -4,8215060,ERS351264,,TAGGCATG,AGAGTAGA,,qPCR only,TAGGCATGAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell42 8215060,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351264,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706431,,mES_ai2_s2_cell42,mES_ai2_s2_cell42,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,42, -4,8215061,ERS351266,,CTCTCTAC,AGAGTAGA,,qPCR only,CTCTCTACAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell43 8215061,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351266,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706432,,mES_ai2_s2_cell43,mES_ai2_s2_cell43,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,43, -4,8215062,ERS351267,,CAGAGAGG,AGAGTAGA,,qPCR only,CAGAGAGGAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell44 8215062,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351267,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706433,,mES_ai2_s2_cell44,mES_ai2_s2_cell44,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,44, -4,8215063,ERS351268,,GCTACGCT,AGAGTAGA,,qPCR only,GCTACGCTAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell45 8215063,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351268,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706434,,mES_ai2_s2_cell45,mES_ai2_s2_cell45,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,45, -4,8215064,ERS351270,,CGAGGCTG,AGAGTAGA,,qPCR only,CGAGGCTGAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell46 8215064,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351270,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706435,,mES_ai2_s2_cell46,mES_ai2_s2_cell46,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,46, -4,8215065,ERS351272,,AAGAGGCA,AGAGTAGA,,qPCR only,AAGAGGCAAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell47 8215065,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351272,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706436,,mES_ai2_s2_cell47,mES_ai2_s2_cell47,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,47, -4,8215066,ERS351273,,GTAGAGGA,AGAGTAGA,,qPCR only,GTAGAGGAAGAGTAGA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell48 8215066,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351273,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706437,,mES_ai2_s2_cell48,mES_ai2_s2_cell48,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,48, -4,8215067,ERS351275,,TAAGGCGA,GTAAGGAG,,qPCR only,TAAGGCGAGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell49 8215067,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351275,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706438,,mES_ai2_s2_cell49,mES_ai2_s2_cell49,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,49, -4,8215068,ERS351277,,CGTACTAG,GTAAGGAG,,qPCR only,CGTACTAGGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell50 8215068,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351277,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706439,,mES_ai2_s2_cell50,mES_ai2_s2_cell50,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,50, -4,8215069,ERS351278,,AGGCAGAA,GTAAGGAG,,qPCR only,AGGCAGAAGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell51 8215069,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351278,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706440,,mES_ai2_s2_cell51,mES_ai2_s2_cell51,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,51, -4,8215070,ERS351279,,TCCTGAGC,GTAAGGAG,,qPCR only,TCCTGAGCGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell52 8215070,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351279,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706441,,mES_ai2_s2_cell52,mES_ai2_s2_cell52,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,52, -4,8215071,ERS351280,,GGACTCCT,GTAAGGAG,,qPCR only,GGACTCCTGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell53 8215071,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351280,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706442,,mES_ai2_s2_cell53,mES_ai2_s2_cell53,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,53, -4,8215072,ERS351281,,TAGGCATG,GTAAGGAG,,qPCR only,TAGGCATGGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell54 8215072,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351281,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706443,,mES_ai2_s2_cell54,mES_ai2_s2_cell54,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,54, -4,8215073,ERS351282,,CTCTCTAC,GTAAGGAG,,qPCR only,CTCTCTACGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell55 8215073,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351282,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706444,,mES_ai2_s2_cell55,mES_ai2_s2_cell55,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,55, -4,8215074,ERS351274,,CAGAGAGG,GTAAGGAG,,qPCR only,CAGAGAGGGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell56 8215074,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351274,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706445,,mES_ai2_s2_cell56,mES_ai2_s2_cell56,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,56, -4,8215075,ERS351276,,GCTACGCT,GTAAGGAG,,qPCR only,GCTACGCTGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell57 8215075,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351276,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706446,,mES_ai2_s2_cell57,mES_ai2_s2_cell57,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,57, -4,8215076,ERS351285,,CGAGGCTG,GTAAGGAG,,qPCR only,CGAGGCTGGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell58 8215076,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351285,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706447,,mES_ai2_s2_cell58,mES_ai2_s2_cell58,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,58, -4,8215077,ERS351286,,AAGAGGCA,GTAAGGAG,,qPCR only,AAGAGGCAGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell59 8215077,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351286,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706448,,mES_ai2_s2_cell59,mES_ai2_s2_cell59,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,59, -4,8215078,ERS351287,,GTAGAGGA,GTAAGGAG,,qPCR only,GTAGAGGAGTAAGGAG,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell60 8215078,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351287,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706449,,mES_ai2_s2_cell60,mES_ai2_s2_cell60,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,60, -4,8215079,ERS351288,,TAAGGCGA,ACTGCATA,,qPCR only,TAAGGCGAACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell61 8215079,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351288,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706450,,mES_ai2_s2_cell61,mES_ai2_s2_cell61,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,61, -4,8215080,ERS351289,,CGTACTAG,ACTGCATA,,qPCR only,CGTACTAGACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell62 8215080,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351289,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706451,,mES_ai2_s2_cell62,mES_ai2_s2_cell62,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,62, -4,8215081,ERS351290,,AGGCAGAA,ACTGCATA,,qPCR only,AGGCAGAAACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell63 8215081,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351290,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706452,,mES_ai2_s2_cell63,mES_ai2_s2_cell63,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,63, -4,8215082,ERS351283,,TCCTGAGC,ACTGCATA,,qPCR only,TCCTGAGCACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell64 8215082,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351283,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706453,,mES_ai2_s2_cell64,mES_ai2_s2_cell64,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,64, -4,8215083,ERS351284,,GGACTCCT,ACTGCATA,,qPCR only,GGACTCCTACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell65 8215083,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351284,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706454,,mES_ai2_s2_cell65,mES_ai2_s2_cell65,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,65, -4,8215084,ERS351292,,TAGGCATG,ACTGCATA,,qPCR only,TAGGCATGACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell66 8215084,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351292,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706455,,mES_ai2_s2_cell66,mES_ai2_s2_cell66,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,66, -4,8215085,ERS351293,,CTCTCTAC,ACTGCATA,,qPCR only,CTCTCTACACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell67 8215085,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351293,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706456,,mES_ai2_s2_cell67,mES_ai2_s2_cell67,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,67, -4,8215086,ERS351294,,CAGAGAGG,ACTGCATA,,qPCR only,CAGAGAGGACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell68 8215086,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351294,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706457,,mES_ai2_s2_cell68,mES_ai2_s2_cell68,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,68, -4,8215087,ERS351295,,GCTACGCT,ACTGCATA,,qPCR only,GCTACGCTACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell69 8215087,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351295,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706458,,mES_ai2_s2_cell69,mES_ai2_s2_cell69,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,69, -4,8215088,ERS351296,,CGAGGCTG,ACTGCATA,,qPCR only,CGAGGCTGACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell70 8215088,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351296,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706459,,mES_ai2_s2_cell70,mES_ai2_s2_cell70,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,70, -4,8215089,ERS351297,,AAGAGGCA,ACTGCATA,,qPCR only,AAGAGGCAACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell71 8215089,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351297,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706460,,mES_ai2_s2_cell71,mES_ai2_s2_cell71,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,71, -4,8215090,ERS351291,,GTAGAGGA,ACTGCATA,,qPCR only,GTAGAGGAACTGCATA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell72 8215090,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351291,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706461,,mES_ai2_s2_cell72,mES_ai2_s2_cell72,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,72, -4,8215091,ERS351299,,TAAGGCGA,AAGGAGTA,,qPCR only,TAAGGCGAAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell73 8215091,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351299,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706462,,mES_ai2_s2_cell73,mES_ai2_s2_cell73,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,73, -4,8215092,ERS351301,,CGTACTAG,AAGGAGTA,,qPCR only,CGTACTAGAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell74 8215092,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351301,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706463,,mES_ai2_s2_cell74,mES_ai2_s2_cell74,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,74, -4,8215093,ERS351302,,AGGCAGAA,AAGGAGTA,,qPCR only,AGGCAGAAAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell75 8215093,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351302,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706464,,mES_ai2_s2_cell75,mES_ai2_s2_cell75,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,75, -4,8215094,ERS351303,,TCCTGAGC,AAGGAGTA,,qPCR only,TCCTGAGCAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell76 8215094,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351303,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706465,,mES_ai2_s2_cell76,mES_ai2_s2_cell76,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,76, -4,8215095,ERS351304,,GGACTCCT,AAGGAGTA,,qPCR only,GGACTCCTAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell77 8215095,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351304,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706466,,mES_ai2_s2_cell77,mES_ai2_s2_cell77,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,77, -4,8215096,ERS351305,,TAGGCATG,AAGGAGTA,,qPCR only,TAGGCATGAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell78 8215096,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351305,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706467,,mES_ai2_s2_cell78,mES_ai2_s2_cell78,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,78, -4,8215097,ERS351306,,CTCTCTAC,AAGGAGTA,,qPCR only,CTCTCTACAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell79 8215097,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351306,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706468,,mES_ai2_s2_cell79,mES_ai2_s2_cell79,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,79, -4,8215098,ERS351298,,CAGAGAGG,AAGGAGTA,,qPCR only,CAGAGAGGAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell80 8215098,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351298,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706469,,mES_ai2_s2_cell80,mES_ai2_s2_cell80,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,80, -4,8215099,ERS351300,,GCTACGCT,AAGGAGTA,,qPCR only,GCTACGCTAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell81 8215099,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351300,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706470,,mES_ai2_s2_cell81,mES_ai2_s2_cell81,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,81, -4,8215100,ERS351309,,CGAGGCTG,AAGGAGTA,,qPCR only,CGAGGCTGAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell82 8215100,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351309,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706471,,mES_ai2_s2_cell82,mES_ai2_s2_cell82,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,82, -4,8215101,ERS351310,,AAGAGGCA,AAGGAGTA,,qPCR only,AAGAGGCAAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell83 8215101,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351310,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706472,,mES_ai2_s2_cell83,mES_ai2_s2_cell83,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,83, -4,8215102,ERS351311,,GTAGAGGA,AAGGAGTA,,qPCR only,GTAGAGGAAAGGAGTA,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell84 8215102,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351311,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706473,,mES_ai2_s2_cell84,mES_ai2_s2_cell84,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,84, -4,8215103,ERS351312,,TAAGGCGA,CTAAGCCT,,qPCR only,TAAGGCGACTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell85 8215103,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351312,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706474,,mES_ai2_s2_cell85,mES_ai2_s2_cell85,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,85, -4,8215104,ERS351313,,CGTACTAG,CTAAGCCT,,qPCR only,CGTACTAGCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell86 8215104,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351313,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706475,,mES_ai2_s2_cell86,mES_ai2_s2_cell86,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,86, -4,8215105,ERS351314,,AGGCAGAA,CTAAGCCT,,qPCR only,AGGCAGAACTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell87 8215105,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351314,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706476,,mES_ai2_s2_cell87,mES_ai2_s2_cell87,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,87, -4,8215106,ERS351307,,TCCTGAGC,CTAAGCCT,,qPCR only,TCCTGAGCCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell88 8215106,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351307,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706477,,mES_ai2_s2_cell88,mES_ai2_s2_cell88,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,88, -4,8215107,ERS351308,,GGACTCCT,CTAAGCCT,,qPCR only,GGACTCCTCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell89 8215107,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351308,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706478,,mES_ai2_s2_cell89,mES_ai2_s2_cell89,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,89, -4,8215108,ERS351315,,TAGGCATG,CTAAGCCT,,qPCR only,TAGGCATGCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell90 8215108,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351315,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706479,,mES_ai2_s2_cell90,mES_ai2_s2_cell90,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,90, -4,8215109,ERS351316,,CTCTCTAC,CTAAGCCT,,qPCR only,CTCTCTACCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell91 8215109,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351316,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706480,,mES_ai2_s2_cell91,mES_ai2_s2_cell91,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,91, -4,8215110,ERS351317,,CAGAGAGG,CTAAGCCT,,qPCR only,CAGAGAGGCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell92 8215110,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351317,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706481,,mES_ai2_s2_cell92,mES_ai2_s2_cell92,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,92, -4,8215111,ERS351318,,GCTACGCT,CTAAGCCT,,qPCR only,GCTACGCTCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell93 8215111,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351318,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706482,,mES_ai2_s2_cell93,mES_ai2_s2_cell93,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,93, -4,8215112,ERS351319,,CGAGGCTG,CTAAGCCT,,qPCR only,CGAGGCTGCTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell94 8215112,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351319,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706483,,mES_ai2_s2_cell94,mES_ai2_s2_cell94,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,94, -4,8215113,ERS351320,,AAGAGGCA,CTAAGCCT,,qPCR only,AAGAGGCACTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell95 8215113,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351320,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706484,,mES_ai2_s2_cell95,mES_ai2_s2_cell95,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,95, -4,8215114,ERS351321,,GTAGAGGA,CTAAGCCT,,qPCR only,GTAGAGGACTAAGCCT,,ncb@sanger.ac.uk ola@ebi.ac.uk,,ncb@sanger.ac.uk,ola@ebi.ac.uk,,0,0,,,mES_ai2_s2_cell96 8215114,mus musculus,10090,S0917,1366,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,standard,,,from:300 to:1000,ERS351321,,Mus Musculus,,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706485,,mES_ai2_s2_cell96,mES_ai2_s2_cell96,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes%2C e.g. Nanog%2C in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study%2C we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum%2FLIF and 2i%2FLIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network.%0A ,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,96, -4,6200285,phiX_for_spiked_buffers,,ACAACGCAAT,,,,ACAACGCAAT,,hps@sanger.ac.uk,,hps@sanger.ac.uk,hps@sanger.ac.uk,,1,0,,,PhiX_PS_20120919,,,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,,,168,,1,0,0,None,198,Illumina Controls,,,,168, -5,8269740,EGAN00001173643,,,,,No PCR,,,cdt@sanger.ac.uk cs4@sanger.ac.uk je6@sanger.ac.uk las@sanger.ac.uk lm5@sanger.ac.uk sm2@sanger.ac.uk som@sanger.ac.uk,cdt@sanger.ac.uk je6@sanger.ac.uk las@sanger.ac.uk som@sanger.ac.uk,cdt@sanger.ac.uk cs4@sanger.ac.uk lm5@sanger.ac.uk sm2@sanger.ac.uk,sm2@sanger.ac.uk,,0,0,8381740,0,PD14393b_wg 8269740,Human,9606,S0814,1422,CGP Core Sequencing 10%2F13 to 09%2F14,standard,,5676016,from:300 to:500,EGAN00001173643,,Homo sapiens,,,,,1712041,,PD14393b_wg,PD14393b,,,168,EGAS00001000290,1,0,0,Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myeloproliferative Disease samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations%2C insertions%2C deletions as well as larger structural variants and genomic rearrangements. ,2239,MPN Whole Genomes,Homo_sapiens (CGP_GRCh37.NCBI.allchr_MT),,Myeloproliferative Disease Whole Genomes,, -6,8324592,ERS354532,,GAGATTCC,TAATCTTA,,Pre-quality controlled,GAGATTCCTAATCTTA,,ms27@sanger.ac.uk ncb@sanger.ac.uk,,ncb@sanger.ac.uk,ms27@sanger.ac.uk,,0,0,,,T_BCM1_F4 8324592,Mouse,10090,S1553,1238,Mouse model to quantify genotype-epigenotype variations,standard,,,from:100 to:1000,ERS354532,,Mus musculus,,,RNA,,1694494,,T_BCM1_F4,RT_37,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression%2C this study has been initiated using two inbred strains of mice%2C C57BL%2F6J and CAST%2FEij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL%2F6J and CAST%2FEij mice as well as CAST%2FBL6 and BL6%2FCAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids.%0A %0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),,Mouse model to quantify genotype-epigenotype variations ,64, -6,8324593,ERS354533,,ATTCAGAA,TAATCTTA,,Pre-quality controlled,ATTCAGAATAATCTTA,,ms27@sanger.ac.uk ncb@sanger.ac.uk,,ncb@sanger.ac.uk,ms27@sanger.ac.uk,,0,0,,,T_BCM1_F5 8324593,Mouse,10090,S1553,1238,Mouse model to quantify genotype-epigenotype variations,standard,,,from:100 to:1000,ERS354533,,Mus musculus,,,RNA,,1694495,,T_BCM1_F5,RT_38,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression%2C this study has been initiated using two inbred strains of mice%2C C57BL%2F6J and CAST%2FEij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL%2F6J and CAST%2FEij mice as well as CAST%2FBL6 and BL6%2FCAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids.%0A %0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),,Mouse model to quantify genotype-epigenotype variations ,65, -6,6200285,phiX_for_spiked_buffers,,ACAACGCAAT,,,,ACAACGCAAT,,hps@sanger.ac.uk,,hps@sanger.ac.uk,hps@sanger.ac.uk,,1,0,,,PhiX_PS_20120919,,,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,,,168,,1,0,0,None,198,Illumina Controls,,,,168, -7,8324594,ERS354534,,GAGATTCC,CAGGACGT,,Pre-quality controlled,GAGATTCCCAGGACGT,,ms27@sanger.ac.uk ncb@sanger.ac.uk,,ncb@sanger.ac.uk,ms27@sanger.ac.uk,,0,0,,,T_CBF1_G4 8324594,Mouse,10090,S1553,1238,Mouse model to quantify genotype-epigenotype variations,standard,,,from:100 to:1000,ERS354534,,Mus musculus,,,RNA,,1694496,,T_CBF1_G4,RT_39,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression%2C this study has been initiated using two inbred strains of mice%2C C57BL%2F6J and CAST%2FEij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL%2F6J and CAST%2FEij mice as well as CAST%2FBL6 and BL6%2FCAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids.%0A %0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),,Mouse model to quantify genotype-epigenotype variations ,76, -7,8324595,ERS354535,,ATTCAGAA,CAGGACGT,,Pre-quality controlled,ATTCAGAACAGGACGT,,ms27@sanger.ac.uk ncb@sanger.ac.uk,,ncb@sanger.ac.uk,ms27@sanger.ac.uk,,0,0,,,T_CBF1_G5 8324595,Mouse,10090,S1553,1238,Mouse model to quantify genotype-epigenotype variations,standard,,,from:100 to:1000,ERS354535,,Mus musculus,,,RNA,,1694497,,T_CBF1_G5,RT_40,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression%2C this study has been initiated using two inbred strains of mice%2C C57BL%2F6J and CAST%2FEij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL%2F6J and CAST%2FEij mice as well as CAST%2FBL6 and BL6%2FCAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids.%0A %0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),,Mouse model to quantify genotype-epigenotype variations ,77, -7,6200285,phiX_for_spiked_buffers,,ACAACGCAAT,,,,ACAACGCAAT,,hps@sanger.ac.uk,,hps@sanger.ac.uk,hps@sanger.ac.uk,,1,0,,,PhiX_PS_20120919,,,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,,,168,,1,0,0,None,198,Illumina Controls,,,,168, -8,8324596,ERS354536,,GAGATTCC,GTACTGAC,,Pre-quality controlled,GAGATTCCGTACTGAC,,ms27@sanger.ac.uk ncb@sanger.ac.uk,,ncb@sanger.ac.uk,ms27@sanger.ac.uk,,0,0,,,T_CBM2_H4 8324596,Mouse,10090,S1553,1238,Mouse model to quantify genotype-epigenotype variations,standard,,,from:100 to:1000,ERS354536,,Mus musculus,,,RNA,,1694498,,T_CBM2_H4,RT_41,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression%2C this study has been initiated using two inbred strains of mice%2C C57BL%2F6J and CAST%2FEij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL%2F6J and CAST%2FEij mice as well as CAST%2FBL6 and BL6%2FCAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids.%0A %0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),,Mouse model to quantify genotype-epigenotype variations ,88, -8,8324597,ERS354537,,ATTCAGAA,GTACTGAC,,Pre-quality controlled,ATTCAGAAGTACTGAC,,ms27@sanger.ac.uk ncb@sanger.ac.uk,,ncb@sanger.ac.uk,ms27@sanger.ac.uk,,0,0,,,T_CBM2_H5 8324597,Mouse,10090,S1553,1238,Mouse model to quantify genotype-epigenotype variations,standard,,,from:100 to:1000,ERS354537,,Mus musculus,,,RNA,,1694499,,T_CBM2_H5,RT_42,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression%2C this study has been initiated using two inbred strains of mice%2C C57BL%2F6J and CAST%2FEij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL%2F6J and CAST%2FEij mice as well as CAST%2FBL6 and BL6%2FCAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids.%0A %0AThis data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),,Mouse model to quantify genotype-epigenotype variations ,89, -8,6200285,phiX_for_spiked_buffers,,ACAACGCAAT,,,,ACAACGCAAT,,hps@sanger.ac.uk,,hps@sanger.ac.uk,hps@sanger.ac.uk,,1,0,,,PhiX_PS_20120919,,,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,,,168,,1,0,0,None,198,Illumina Controls,,,,168, +1,7809257,ERS323818,,,,,No PCR,,,,,,,,0,0,8381746,0,7809257,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323818,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660679,,Hc_4_BC4_P2_5046_340285,Haemonchus contortus MHco3%2F4.BC4(P2)-5046,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +2,7809258,ERS323819,,,,,No PCR,,,,,,,,0,0,8381744,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +3,7809258,ERS323819,,,,,No PCR,,,,,,,,0,0,8381745,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +4,8215019,ERS351213,,TAAGGCGA,TAGATCGC,,qPCR only,TAAGGCGATAGATCGC,,,,,,,0,0,8381739,0,8215019,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351213,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706390,,mES_ai2_s2_cell1,mES_ai2_s2_cell1,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,1, +4,8215020,ERS351214,,CGTACTAG,TAGATCGC,,qPCR only,CGTACTAGTAGATCGC,,,,,,,0,0,8381739,0,8215020,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351214,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706391,,mES_ai2_s2_cell2,mES_ai2_s2_cell2,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,2, +4,8215021,ERS351221,,AGGCAGAA,TAGATCGC,,qPCR only,AGGCAGAATAGATCGC,,,,,,,0,0,8381739,0,8215021,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351221,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706392,,mES_ai2_s2_cell3,mES_ai2_s2_cell3,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,3, +4,8215022,ERS351222,,TCCTGAGC,TAGATCGC,,qPCR only,TCCTGAGCTAGATCGC,,,,,,,0,0,8381739,0,8215022,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351222,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706393,,mES_ai2_s2_cell4,mES_ai2_s2_cell4,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,4, +4,8215023,ERS351223,,GGACTCCT,TAGATCGC,,qPCR only,GGACTCCTTAGATCGC,,,,,,,0,0,8381739,0,8215023,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351223,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706394,,mES_ai2_s2_cell5,mES_ai2_s2_cell5,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,5, +4,8215024,ERS351224,,TAGGCATG,TAGATCGC,,qPCR only,TAGGCATGTAGATCGC,,,,,,,0,0,8381739,0,8215024,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351224,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706395,,mES_ai2_s2_cell6,mES_ai2_s2_cell6,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,6, +4,8215025,ERS351225,,CTCTCTAC,TAGATCGC,,qPCR only,CTCTCTACTAGATCGC,,,,,,,0,0,8381739,0,8215025,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351225,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706396,,mES_ai2_s2_cell7,mES_ai2_s2_cell7,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,7, +4,8215026,ERS351218,,CAGAGAGG,TAGATCGC,,qPCR only,CAGAGAGGTAGATCGC,,,,,,,0,0,8381739,0,8215026,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351218,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706397,,mES_ai2_s2_cell8,mES_ai2_s2_cell8,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,8, +4,8215027,ERS351219,,GCTACGCT,TAGATCGC,,qPCR only,GCTACGCTTAGATCGC,,,,,,,0,0,8381739,0,8215027,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351219,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706398,,mES_ai2_s2_cell9,mES_ai2_s2_cell9,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,9, +4,8215028,ERS351220,,CGAGGCTG,TAGATCGC,,qPCR only,CGAGGCTGTAGATCGC,,,,,,,0,0,8381739,0,8215028,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351220,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706399,,mES_ai2_s2_cell10,mES_ai2_s2_cell10,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,10, +4,8215029,ERS351235,,AAGAGGCA,TAGATCGC,,qPCR only,AAGAGGCATAGATCGC,,,,,,,0,0,8381739,0,8215029,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351235,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706400,,mES_ai2_s2_cell11,mES_ai2_s2_cell11,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,11, +4,8215030,ERS351237,,GTAGAGGA,TAGATCGC,,qPCR only,GTAGAGGATAGATCGC,,,,,,,0,0,8381739,0,8215030,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351237,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706401,,mES_ai2_s2_cell12,mES_ai2_s2_cell12,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,12, +4,8215031,ERS351238,,TAAGGCGA,CTCTCTAT,,qPCR only,TAAGGCGACTCTCTAT,,,,,,,0,0,8381739,0,8215031,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351238,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706402,,mES_ai2_s2_cell13,mES_ai2_s2_cell13,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,13, +4,8215032,ERS351239,,CGTACTAG,CTCTCTAT,,qPCR only,CGTACTAGCTCTCTAT,,,,,,,0,0,8381739,0,8215032,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351239,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706403,,mES_ai2_s2_cell14,mES_ai2_s2_cell14,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,14, +4,8215033,ERS351241,,AGGCAGAA,CTCTCTAT,,qPCR only,AGGCAGAACTCTCTAT,,,,,,,0,0,8381739,0,8215033,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351241,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706404,,mES_ai2_s2_cell15,mES_ai2_s2_cell15,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,15, +4,8215034,ERS351226,,TCCTGAGC,CTCTCTAT,,qPCR only,TCCTGAGCCTCTCTAT,,,,,,,0,0,8381739,0,8215034,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351226,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706405,,mES_ai2_s2_cell16,mES_ai2_s2_cell16,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,16, +4,8215035,ERS351227,,GGACTCCT,CTCTCTAT,,qPCR only,GGACTCCTCTCTCTAT,,,,,,,0,0,8381739,0,8215035,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351227,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706406,,mES_ai2_s2_cell17,mES_ai2_s2_cell17,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,17, +4,8215036,ERS351234,,TAGGCATG,CTCTCTAT,,qPCR only,TAGGCATGCTCTCTAT,,,,,,,0,0,8381739,0,8215036,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351234,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706407,,mES_ai2_s2_cell18,mES_ai2_s2_cell18,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,18, +4,8215037,ERS351236,,CTCTCTAC,CTCTCTAT,,qPCR only,CTCTCTACCTCTCTAT,,,,,,,0,0,8381739,0,8215037,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351236,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706408,,mES_ai2_s2_cell19,mES_ai2_s2_cell19,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,19, +4,8215038,ERS351247,,CAGAGAGG,CTCTCTAT,,qPCR only,CAGAGAGGCTCTCTAT,,,,,,,0,0,8381739,0,8215038,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351247,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706409,,mES_ai2_s2_cell20,mES_ai2_s2_cell20,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,20, +4,8215039,ERS351249,,GCTACGCT,CTCTCTAT,,qPCR only,GCTACGCTCTCTCTAT,,,,,,,0,0,8381739,0,8215039,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351249,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706410,,mES_ai2_s2_cell21,mES_ai2_s2_cell21,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,21, +4,8215040,ERS351251,,CGAGGCTG,CTCTCTAT,,qPCR only,CGAGGCTGCTCTCTAT,,,,,,,0,0,8381739,0,8215040,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351251,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706411,,mES_ai2_s2_cell22,mES_ai2_s2_cell22,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,22, +4,8215041,ERS351252,,AAGAGGCA,CTCTCTAT,,qPCR only,AAGAGGCACTCTCTAT,,,,,,,0,0,8381739,0,8215041,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351252,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706412,,mES_ai2_s2_cell23,mES_ai2_s2_cell23,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,23, +4,8215042,ERS351242,,GTAGAGGA,CTCTCTAT,,qPCR only,GTAGAGGACTCTCTAT,,,,,,,0,0,8381739,0,8215042,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351242,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706413,,mES_ai2_s2_cell24,mES_ai2_s2_cell24,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,24, +4,8215043,ERS351243,,TAAGGCGA,TATCCTCT,,qPCR only,TAAGGCGATATCCTCT,,,,,,,0,0,8381739,0,8215043,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351243,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706414,,mES_ai2_s2_cell25,mES_ai2_s2_cell25,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,25, +4,8215044,ERS351244,,CGTACTAG,TATCCTCT,,qPCR only,CGTACTAGTATCCTCT,,,,,,,0,0,8381739,0,8215044,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351244,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706415,,mES_ai2_s2_cell26,mES_ai2_s2_cell26,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,26, +4,8215045,ERS351245,,AGGCAGAA,TATCCTCT,,qPCR only,AGGCAGAATATCCTCT,,,,,,,0,0,8381739,0,8215045,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351245,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706416,,mES_ai2_s2_cell27,mES_ai2_s2_cell27,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,27, +4,8215046,ERS351248,,TCCTGAGC,TATCCTCT,,qPCR only,TCCTGAGCTATCCTCT,,,,,,,0,0,8381739,0,8215046,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351248,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706417,,mES_ai2_s2_cell28,mES_ai2_s2_cell28,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,28, +4,8215047,ERS351250,,GGACTCCT,TATCCTCT,,qPCR only,GGACTCCTTATCCTCT,,,,,,,0,0,8381739,0,8215047,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351250,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706418,,mES_ai2_s2_cell29,mES_ai2_s2_cell29,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,29, +4,8215048,ERS351260,,TAGGCATG,TATCCTCT,,qPCR only,TAGGCATGTATCCTCT,,,,,,,0,0,8381739,0,8215048,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351260,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706419,,mES_ai2_s2_cell30,mES_ai2_s2_cell30,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,30, +4,8215049,ERS351261,,CTCTCTAC,TATCCTCT,,qPCR only,CTCTCTACTATCCTCT,,,,,,,0,0,8381739,0,8215049,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351261,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706420,,mES_ai2_s2_cell31,mES_ai2_s2_cell31,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,31, +4,8215050,ERS351254,,CAGAGAGG,TATCCTCT,,qPCR only,CAGAGAGGTATCCTCT,,,,,,,0,0,8381739,0,8215050,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351254,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706421,,mES_ai2_s2_cell32,mES_ai2_s2_cell32,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,32, +4,8215051,ERS351255,,GCTACGCT,TATCCTCT,,qPCR only,GCTACGCTTATCCTCT,,,,,,,0,0,8381739,0,8215051,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351255,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706422,,mES_ai2_s2_cell33,mES_ai2_s2_cell33,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,33, +4,8215052,ERS351256,,CGAGGCTG,TATCCTCT,,qPCR only,CGAGGCTGTATCCTCT,,,,,,,0,0,8381739,0,8215052,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351256,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706423,,mES_ai2_s2_cell34,mES_ai2_s2_cell34,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,34, +4,8215053,ERS351257,,AAGAGGCA,TATCCTCT,,qPCR only,AAGAGGCATATCCTCT,,,,,,,0,0,8381739,0,8215053,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351257,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706424,,mES_ai2_s2_cell35,mES_ai2_s2_cell35,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,35, +4,8215054,ERS351258,,GTAGAGGA,TATCCTCT,,qPCR only,GTAGAGGATATCCTCT,,,,,,,0,0,8381739,0,8215054,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351258,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706425,,mES_ai2_s2_cell36,mES_ai2_s2_cell36,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,36, +4,8215055,ERS351259,,TAAGGCGA,AGAGTAGA,,qPCR only,TAAGGCGAAGAGTAGA,,,,,,,0,0,8381739,0,8215055,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351259,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706426,,mES_ai2_s2_cell37,mES_ai2_s2_cell37,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,37, +4,8215056,ERS351269,,CGTACTAG,AGAGTAGA,,qPCR only,CGTACTAGAGAGTAGA,,,,,,,0,0,8381739,0,8215056,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351269,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706427,,mES_ai2_s2_cell38,mES_ai2_s2_cell38,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,38, +4,8215057,ERS351271,,AGGCAGAA,AGAGTAGA,,qPCR only,AGGCAGAAAGAGTAGA,,,,,,,0,0,8381739,0,8215057,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351271,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706428,,mES_ai2_s2_cell39,mES_ai2_s2_cell39,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,39, +4,8215058,ERS351262,,TCCTGAGC,AGAGTAGA,,qPCR only,TCCTGAGCAGAGTAGA,,,,,,,0,0,8381739,0,8215058,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351262,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706429,,mES_ai2_s2_cell40,mES_ai2_s2_cell40,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,40, +4,8215059,ERS351263,,GGACTCCT,AGAGTAGA,,qPCR only,GGACTCCTAGAGTAGA,,,,,,,0,0,8381739,0,8215059,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351263,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706430,,mES_ai2_s2_cell41,mES_ai2_s2_cell41,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,41, +4,8215060,ERS351264,,TAGGCATG,AGAGTAGA,,qPCR only,TAGGCATGAGAGTAGA,,,,,,,0,0,8381739,0,8215060,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351264,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706431,,mES_ai2_s2_cell42,mES_ai2_s2_cell42,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,42, +4,8215061,ERS351266,,CTCTCTAC,AGAGTAGA,,qPCR only,CTCTCTACAGAGTAGA,,,,,,,0,0,8381739,0,8215061,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351266,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706432,,mES_ai2_s2_cell43,mES_ai2_s2_cell43,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,43, +4,8215062,ERS351267,,CAGAGAGG,AGAGTAGA,,qPCR only,CAGAGAGGAGAGTAGA,,,,,,,0,0,8381739,0,8215062,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351267,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706433,,mES_ai2_s2_cell44,mES_ai2_s2_cell44,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,44, +4,8215063,ERS351268,,GCTACGCT,AGAGTAGA,,qPCR only,GCTACGCTAGAGTAGA,,,,,,,0,0,8381739,0,8215063,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351268,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706434,,mES_ai2_s2_cell45,mES_ai2_s2_cell45,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,45, +4,8215064,ERS351270,,CGAGGCTG,AGAGTAGA,,qPCR only,CGAGGCTGAGAGTAGA,,,,,,,0,0,8381739,0,8215064,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351270,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706435,,mES_ai2_s2_cell46,mES_ai2_s2_cell46,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,46, +4,8215065,ERS351272,,AAGAGGCA,AGAGTAGA,,qPCR only,AAGAGGCAAGAGTAGA,,,,,,,0,0,8381739,0,8215065,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351272,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706436,,mES_ai2_s2_cell47,mES_ai2_s2_cell47,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,47, +4,8215066,ERS351273,,GTAGAGGA,AGAGTAGA,,qPCR only,GTAGAGGAAGAGTAGA,,,,,,,0,0,8381739,0,8215066,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351273,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706437,,mES_ai2_s2_cell48,mES_ai2_s2_cell48,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,48, +4,8215067,ERS351275,,TAAGGCGA,GTAAGGAG,,qPCR only,TAAGGCGAGTAAGGAG,,,,,,,0,0,8381739,0,8215067,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351275,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706438,,mES_ai2_s2_cell49,mES_ai2_s2_cell49,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,49, +4,8215068,ERS351277,,CGTACTAG,GTAAGGAG,,qPCR only,CGTACTAGGTAAGGAG,,,,,,,0,0,8381739,0,8215068,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351277,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706439,,mES_ai2_s2_cell50,mES_ai2_s2_cell50,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,50, +4,8215069,ERS351278,,AGGCAGAA,GTAAGGAG,,qPCR only,AGGCAGAAGTAAGGAG,,,,,,,0,0,8381739,0,8215069,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351278,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706440,,mES_ai2_s2_cell51,mES_ai2_s2_cell51,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,51, +4,8215070,ERS351279,,TCCTGAGC,GTAAGGAG,,qPCR only,TCCTGAGCGTAAGGAG,,,,,,,0,0,8381739,0,8215070,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351279,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706441,,mES_ai2_s2_cell52,mES_ai2_s2_cell52,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,52, +4,8215071,ERS351280,,GGACTCCT,GTAAGGAG,,qPCR only,GGACTCCTGTAAGGAG,,,,,,,0,0,8381739,0,8215071,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351280,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706442,,mES_ai2_s2_cell53,mES_ai2_s2_cell53,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,53, +4,8215072,ERS351281,,TAGGCATG,GTAAGGAG,,qPCR only,TAGGCATGGTAAGGAG,,,,,,,0,0,8381739,0,8215072,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351281,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706443,,mES_ai2_s2_cell54,mES_ai2_s2_cell54,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,54, +4,8215073,ERS351282,,CTCTCTAC,GTAAGGAG,,qPCR only,CTCTCTACGTAAGGAG,,,,,,,0,0,8381739,0,8215073,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351282,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706444,,mES_ai2_s2_cell55,mES_ai2_s2_cell55,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,55, +4,8215074,ERS351274,,CAGAGAGG,GTAAGGAG,,qPCR only,CAGAGAGGGTAAGGAG,,,,,,,0,0,8381739,0,8215074,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351274,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706445,,mES_ai2_s2_cell56,mES_ai2_s2_cell56,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,56, +4,8215075,ERS351276,,GCTACGCT,GTAAGGAG,,qPCR only,GCTACGCTGTAAGGAG,,,,,,,0,0,8381739,0,8215075,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351276,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706446,,mES_ai2_s2_cell57,mES_ai2_s2_cell57,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,57, +4,8215076,ERS351285,,CGAGGCTG,GTAAGGAG,,qPCR only,CGAGGCTGGTAAGGAG,,,,,,,0,0,8381739,0,8215076,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351285,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706447,,mES_ai2_s2_cell58,mES_ai2_s2_cell58,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,58, +4,8215077,ERS351286,,AAGAGGCA,GTAAGGAG,,qPCR only,AAGAGGCAGTAAGGAG,,,,,,,0,0,8381739,0,8215077,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351286,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706448,,mES_ai2_s2_cell59,mES_ai2_s2_cell59,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,59, +4,8215078,ERS351287,,GTAGAGGA,GTAAGGAG,,qPCR only,GTAGAGGAGTAAGGAG,,,,,,,0,0,8381739,0,8215078,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351287,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706449,,mES_ai2_s2_cell60,mES_ai2_s2_cell60,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,60, +4,8215079,ERS351288,,TAAGGCGA,ACTGCATA,,qPCR only,TAAGGCGAACTGCATA,,,,,,,0,0,8381739,0,8215079,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351288,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706450,,mES_ai2_s2_cell61,mES_ai2_s2_cell61,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,61, +4,8215080,ERS351289,,CGTACTAG,ACTGCATA,,qPCR only,CGTACTAGACTGCATA,,,,,,,0,0,8381739,0,8215080,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351289,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706451,,mES_ai2_s2_cell62,mES_ai2_s2_cell62,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,62, +4,8215081,ERS351290,,AGGCAGAA,ACTGCATA,,qPCR only,AGGCAGAAACTGCATA,,,,,,,0,0,8381739,0,8215081,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351290,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706452,,mES_ai2_s2_cell63,mES_ai2_s2_cell63,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,63, +4,8215082,ERS351283,,TCCTGAGC,ACTGCATA,,qPCR only,TCCTGAGCACTGCATA,,,,,,,0,0,8381739,0,8215082,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351283,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706453,,mES_ai2_s2_cell64,mES_ai2_s2_cell64,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,64, +4,8215083,ERS351284,,GGACTCCT,ACTGCATA,,qPCR only,GGACTCCTACTGCATA,,,,,,,0,0,8381739,0,8215083,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351284,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706454,,mES_ai2_s2_cell65,mES_ai2_s2_cell65,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,65, +4,8215084,ERS351292,,TAGGCATG,ACTGCATA,,qPCR only,TAGGCATGACTGCATA,,,,,,,0,0,8381739,0,8215084,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351292,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706455,,mES_ai2_s2_cell66,mES_ai2_s2_cell66,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,66, +4,8215085,ERS351293,,CTCTCTAC,ACTGCATA,,qPCR only,CTCTCTACACTGCATA,,,,,,,0,0,8381739,0,8215085,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351293,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706456,,mES_ai2_s2_cell67,mES_ai2_s2_cell67,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,67, +4,8215086,ERS351294,,CAGAGAGG,ACTGCATA,,qPCR only,CAGAGAGGACTGCATA,,,,,,,0,0,8381739,0,8215086,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351294,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706457,,mES_ai2_s2_cell68,mES_ai2_s2_cell68,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,68, +4,8215087,ERS351295,,GCTACGCT,ACTGCATA,,qPCR only,GCTACGCTACTGCATA,,,,,,,0,0,8381739,0,8215087,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351295,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706458,,mES_ai2_s2_cell69,mES_ai2_s2_cell69,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,69, +4,8215088,ERS351296,,CGAGGCTG,ACTGCATA,,qPCR only,CGAGGCTGACTGCATA,,,,,,,0,0,8381739,0,8215088,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351296,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706459,,mES_ai2_s2_cell70,mES_ai2_s2_cell70,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,70, +4,8215089,ERS351297,,AAGAGGCA,ACTGCATA,,qPCR only,AAGAGGCAACTGCATA,,,,,,,0,0,8381739,0,8215089,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351297,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706460,,mES_ai2_s2_cell71,mES_ai2_s2_cell71,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,71, +4,8215090,ERS351291,,GTAGAGGA,ACTGCATA,,qPCR only,GTAGAGGAACTGCATA,,,,,,,0,0,8381739,0,8215090,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351291,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706461,,mES_ai2_s2_cell72,mES_ai2_s2_cell72,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,72, +4,8215091,ERS351299,,TAAGGCGA,AAGGAGTA,,qPCR only,TAAGGCGAAAGGAGTA,,,,,,,0,0,8381739,0,8215091,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351299,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706462,,mES_ai2_s2_cell73,mES_ai2_s2_cell73,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,73, +4,8215092,ERS351301,,CGTACTAG,AAGGAGTA,,qPCR only,CGTACTAGAAGGAGTA,,,,,,,0,0,8381739,0,8215092,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351301,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706463,,mES_ai2_s2_cell74,mES_ai2_s2_cell74,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,74, +4,8215093,ERS351302,,AGGCAGAA,AAGGAGTA,,qPCR only,AGGCAGAAAAGGAGTA,,,,,,,0,0,8381739,0,8215093,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351302,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706464,,mES_ai2_s2_cell75,mES_ai2_s2_cell75,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,75, +4,8215094,ERS351303,,TCCTGAGC,AAGGAGTA,,qPCR only,TCCTGAGCAAGGAGTA,,,,,,,0,0,8381739,0,8215094,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351303,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706465,,mES_ai2_s2_cell76,mES_ai2_s2_cell76,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,76, +4,8215095,ERS351304,,GGACTCCT,AAGGAGTA,,qPCR only,GGACTCCTAAGGAGTA,,,,,,,0,0,8381739,0,8215095,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351304,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706466,,mES_ai2_s2_cell77,mES_ai2_s2_cell77,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,77, +4,8215096,ERS351305,,TAGGCATG,AAGGAGTA,,qPCR only,TAGGCATGAAGGAGTA,,,,,,,0,0,8381739,0,8215096,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351305,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706467,,mES_ai2_s2_cell78,mES_ai2_s2_cell78,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,78, +4,8215097,ERS351306,,CTCTCTAC,AAGGAGTA,,qPCR only,CTCTCTACAAGGAGTA,,,,,,,0,0,8381739,0,8215097,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351306,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706468,,mES_ai2_s2_cell79,mES_ai2_s2_cell79,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,79, +4,8215098,ERS351298,,CAGAGAGG,AAGGAGTA,,qPCR only,CAGAGAGGAAGGAGTA,,,,,,,0,0,8381739,0,8215098,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351298,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706469,,mES_ai2_s2_cell80,mES_ai2_s2_cell80,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,80, +4,8215099,ERS351300,,GCTACGCT,AAGGAGTA,,qPCR only,GCTACGCTAAGGAGTA,,,,,,,0,0,8381739,0,8215099,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351300,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706470,,mES_ai2_s2_cell81,mES_ai2_s2_cell81,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,81, +4,8215100,ERS351309,,CGAGGCTG,AAGGAGTA,,qPCR only,CGAGGCTGAAGGAGTA,,,,,,,0,0,8381739,0,8215100,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351309,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706471,,mES_ai2_s2_cell82,mES_ai2_s2_cell82,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,82, +4,8215101,ERS351310,,AAGAGGCA,AAGGAGTA,,qPCR only,AAGAGGCAAAGGAGTA,,,,,,,0,0,8381739,0,8215101,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351310,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706472,,mES_ai2_s2_cell83,mES_ai2_s2_cell83,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,83, +4,8215102,ERS351311,,GTAGAGGA,AAGGAGTA,,qPCR only,GTAGAGGAAAGGAGTA,,,,,,,0,0,8381739,0,8215102,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351311,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706473,,mES_ai2_s2_cell84,mES_ai2_s2_cell84,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,84, +4,8215103,ERS351312,,TAAGGCGA,CTAAGCCT,,qPCR only,TAAGGCGACTAAGCCT,,,,,,,0,0,8381739,0,8215103,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351312,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706474,,mES_ai2_s2_cell85,mES_ai2_s2_cell85,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,85, +4,8215104,ERS351313,,CGTACTAG,CTAAGCCT,,qPCR only,CGTACTAGCTAAGCCT,,,,,,,0,0,8381739,0,8215104,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351313,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706475,,mES_ai2_s2_cell86,mES_ai2_s2_cell86,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,86, +4,8215105,ERS351314,,AGGCAGAA,CTAAGCCT,,qPCR only,AGGCAGAACTAAGCCT,,,,,,,0,0,8381739,0,8215105,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351314,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706476,,mES_ai2_s2_cell87,mES_ai2_s2_cell87,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,87, +4,8215106,ERS351307,,TCCTGAGC,CTAAGCCT,,qPCR only,TCCTGAGCCTAAGCCT,,,,,,,0,0,8381739,0,8215106,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351307,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706477,,mES_ai2_s2_cell88,mES_ai2_s2_cell88,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,88, +4,8215107,ERS351308,,GGACTCCT,CTAAGCCT,,qPCR only,GGACTCCTCTAAGCCT,,,,,,,0,0,8381739,0,8215107,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351308,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706478,,mES_ai2_s2_cell89,mES_ai2_s2_cell89,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,89, +4,8215108,ERS351315,,TAGGCATG,CTAAGCCT,,qPCR only,TAGGCATGCTAAGCCT,,,,,,,0,0,8381739,0,8215108,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351315,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706479,,mES_ai2_s2_cell90,mES_ai2_s2_cell90,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,90, +4,8215109,ERS351316,,CTCTCTAC,CTAAGCCT,,qPCR only,CTCTCTACCTAAGCCT,,,,,,,0,0,8381739,0,8215109,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351316,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706480,,mES_ai2_s2_cell91,mES_ai2_s2_cell91,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,91, +4,8215110,ERS351317,,CAGAGAGG,CTAAGCCT,,qPCR only,CAGAGAGGCTAAGCCT,,,,,,,0,0,8381739,0,8215110,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351317,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706481,,mES_ai2_s2_cell92,mES_ai2_s2_cell92,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,92, +4,8215111,ERS351318,,GCTACGCT,CTAAGCCT,,qPCR only,GCTACGCTCTAAGCCT,,,,,,,0,0,8381739,0,8215111,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351318,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706482,,mES_ai2_s2_cell93,mES_ai2_s2_cell93,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,93, +4,8215112,ERS351319,,CGAGGCTG,CTAAGCCT,,qPCR only,CGAGGCTGCTAAGCCT,,,,,,,0,0,8381739,0,8215112,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351319,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706483,,mES_ai2_s2_cell94,mES_ai2_s2_cell94,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,94, +4,8215113,ERS351320,,AAGAGGCA,CTAAGCCT,,qPCR only,AAGAGGCACTAAGCCT,,,,,,,0,0,8381739,0,8215113,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351320,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706484,,mES_ai2_s2_cell95,mES_ai2_s2_cell95,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,95, +4,8215114,ERS351321,,GTAGAGGA,CTAAGCCT,,qPCR only,GTAGAGGACTAAGCCT,,,,,,,0,0,8381739,0,8215114,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351321,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706485,,mES_ai2_s2_cell96,mES_ai2_s2_cell96,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,96, +4,6200285,6946_4_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381739,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +5,8269740,EGAN00001173643,,,,,No PCR,,,,,,,,0,0,8381740,0,8269740,Human,9606,S0814,,,standard,,,from:300 to:500,EGAN00001173643,,Homo sapiens,0,,,PD14393b,1712041,,PD14393b_wg,PD14393b,,,168,EGAS00001000290,1,0,0,Wholegenome libraries will be prepared.,2239,MPN Whole Genomes,Homo_sapiens (CGP_GRCh37.NCBI.allchr_MT),0,Myeloproliferative Disease Whole Genomes,, +6,8324592,ERS354532,,GAGATTCC,TAATCTTA,,Pre-quality controlled,GAGATTCCTAATCTTA,,,,,,,0,0,8381741,0,8324592,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354532,,Mus musculus,0,,RNA,,1694494,,T_BCM1_F4,RT_37,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,64, +6,8324593,ERS354533,,ATTCAGAA,TAATCTTA,,Pre-quality controlled,ATTCAGAATAATCTTA,,,,,,,0,0,8381741,0,8324593,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354533,,Mus musculus,0,,RNA,,1694495,,T_BCM1_F5,RT_38,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,65, +6,6200285,6946_6_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381741,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +7,8324594,ERS354534,,GAGATTCC,CAGGACGT,,Pre-quality controlled,GAGATTCCCAGGACGT,,,,,,,0,0,8381742,0,8324594,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354534,,Mus musculus,0,,RNA,,1694496,,T_CBF1_G4,RT_39,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,76, +7,8324595,ERS354535,,ATTCAGAA,CAGGACGT,,Pre-quality controlled,ATTCAGAACAGGACGT,,,,,,,0,0,8381742,0,8324595,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354535,,Mus musculus,0,,RNA,,1694497,,T_CBF1_G5,RT_40,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,77, +7,6200285,6946_7_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381742,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +8,8324596,ERS354536,,GAGATTCC,GTACTGAC,,Pre-quality controlled,GAGATTCCGTACTGAC,,,,,,,0,0,8381743,0,8324596,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354536,,Mus musculus,0,,RNA,,1694498,,T_CBM2_H4,RT_41,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,88, +8,8324597,ERS354537,,ATTCAGAA,GTACTGAC,,Pre-quality controlled,ATTCAGAAGTACTGAC,,,,,,,0,0,8381743,0,8324597,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354537,,Mus musculus,0,,RNA,,1694499,,T_CBM2_H5,RT_42,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,89, +8,6200285,6946_8_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381743,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, diff --git a/t/data/samplesheet/6946_extended.csv b/t/data/samplesheet/6946_extended.csv index 74765147..563f3870 100644 --- a/t/data/samplesheet/6946_extended.csv +++ b/t/data/samplesheet/6946_extended.csv @@ -1,14 +1,14 @@ [Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Sample_ID,Sample_Name,GenomeFolder,Index,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -3789278,Salmonella pullorum,,ATCACGTT,,Standard,ATCACGTT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,sp200shear 3789278,Salmonella pullorum,590,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Salmonella pullorum,,,genomic DNA,,1289832,,sp200shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,1, -3789279,Bordetella Pertussis,,CGATGTTT,,Standard,CGATGTTT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,bp200shear 3789279,Bordetella Pertussis,520,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Bordetella Pertussis,,,genomic DNA,,1289833,,bp200shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,2, -3789280,Plasmodium Falciparum,,TTAGGCAT,,Standard,TTAGGCAT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,3D7200shear 3789280,Plasmodium Falciparum,5820,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Plasmodium Falciparum,,,genomic DNA,,1289834,,3D7200shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,3, -3789281,Homo sapiens,,TGACCACT,,Standard,TGACCACT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,human200shear 3789281,Homo sapiens,9606,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Human,,,genomic DNA,,1289835,,human200shear,Homo sapiens,Homo_sapiens (GRCh37_53),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,4, -3789282,Salmonella pullorum,,ACAGTGGT,,Standard,ACAGTGGT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,sp300shear 3789282,Salmonella pullorum,590,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Salmonella pullorum,,,genomic DNA,,1289836,,sp300shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,5, -3789283,Bordetella Pertussis,,GCCAATGT,,Standard,GCCAATGT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,bp300shear 3789283,Bordetella Pertussis,520,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Bordetella Pertussis,,,genomic DNA,,1289837,,bp300shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,6, -3789284,Plasmodium Falciparum,,CAGATCTG,,Standard,CAGATCTG,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,3D7300shear 3789284,Plasmodium Falciparum,5820,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Plasmodium Falciparum,,,genomic DNA,,1289838,,3D7300shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,7, -3789285,Homo sapiens,,ACTTGATG,,Standard,ACTTGATG,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,human300shear 3789285,Homo sapiens,9606,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Human,,,genomic DNA,,1289839,,human300shear,Homo sapiens,Homo_sapiens (GRCh37_53),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,8, -3789286,Salmonella pullorum,,GATCAGCG,,Standard,GATCAGCG,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,sp400shear 3789286,Salmonella pullorum,590,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Salmonella pullorum,,,genomic DNA,,1289840,,sp400shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,9, -3789287,Bordetella Pertussis,,TAGCTTGT,,Standard,TAGCTTGT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,bp400shear 3789287,Bordetella Pertussis,520,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Bordetella Pertussis,,,genomic DNA,,1289841,,bp400shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,10, -3789288,Plasmodium Falciparum,,GGCTACAG,,Standard,GGCTACAG,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,3D7400shear 3789288,Plasmodium Falciparum,5820,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Plasmodium Falciparum,,,genomic DNA,,1289842,,3D7400shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,11, -3789289,Homo sapiens,,CTTGTACT,,Standard,CTTGTACT,,ems@sanger.ac.uk mq1@sanger.ac.uk,,ems@sanger.ac.uk mq1@sanger.ac.uk,mq1@sanger.ac.uk,,0,0,,,human400shear 3789289,Homo sapiens,9606,S0696,678,MQ R and D,standard,,,from:200 to:700,,,Human,,,genomic DNA,,1289843,,human400shear,Homo sapiens,Homo_sapiens (GRCh37_53),,,,1,0,0,- I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. %09%09%09%09%09%0A- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage.%09%09%09%09%09%0A- In theory kapa hifi has higher fidelity than phusion.%09%09%09%09%09,700,Kapa HiFi test,,,hifi test,12, +3789278,Salmonella pullorum,,ATCACGTT,,Standard,ATCACGTT,,,,,,,0,0,3789299,0,3789278,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289832,,sp200shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,1, +3789279,Bordetella Pertussis,,CGATGTTT,,Standard,CGATGTTT,,,,,,,0,0,3789299,0,3789279,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289833,,bp200shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,2, +3789280,Plasmodium Falciparum,,TTAGGCAT,,Standard,TTAGGCAT,,,,,,,0,0,3789299,0,3789280,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289834,,3D7200shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,3, +3789281,Homo sapiens,,TGACCACT,,Standard,TGACCACT,,,,,,,0,0,3789299,0,3789281,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289835,,human200shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,4, +3789282,Salmonella pullorum,,ACAGTGGT,,Standard,ACAGTGGT,,,,,,,0,0,3789299,0,3789282,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289836,,sp300shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,5, +3789283,Bordetella Pertussis,,GCCAATGT,,Standard,GCCAATGT,,,,,,,0,0,3789299,0,3789283,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289837,,bp300shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,6, +3789284,Plasmodium Falciparum,,CAGATCTG,,Standard,CAGATCTG,,,,,,,0,0,3789299,0,3789284,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289838,,3D7300shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,7, +3789285,Homo sapiens,,ACTTGATG,,Standard,ACTTGATG,,,,,,,0,0,3789299,0,3789285,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289839,,human300shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,8, +3789286,Salmonella pullorum,,GATCAGCG,,Standard,GATCAGCG,,,,,,,0,0,3789299,0,3789286,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289840,,sp400shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,9, +3789287,Bordetella Pertussis,,TAGCTTGT,,Standard,TAGCTTGT,,,,,,,0,0,3789299,0,3789287,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289841,,bp400shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,10, +3789288,Plasmodium Falciparum,,GGCTACAG,,Standard,GGCTACAG,,,,,,,0,0,3789299,0,3789288,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289842,,3D7400shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,11, +3789289,Homo sapiens,,CTTGTACT,,Standard,CTTGTACT,,,,,,,0,0,3789299,0,3789289,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289843,,human400shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,12, diff --git a/t/data/samplesheet/7007_extended.csv b/t/data/samplesheet/7007_extended.csv index 00208b36..df0f87c3 100644 --- a/t/data/samplesheet/7007_extended.csv +++ b/t/data/samplesheet/7007_extended.csv @@ -1,3 +1,3 @@ [Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -3789277,Strongyloides ratti,,,qPCR only,,,dg8@sanger.ac.uk neh@sanger.ac.uk,,dg8@sanger.ac.uk neh@sanger.ac.uk,neh@sanger.ac.uk,,0,0,3911772,0,SriL3_66K_212889 3789277,Strongyloides ratti,34506,S0702,521,Strongyloides ratti transcriptome,standard,pass,3642560,from:300 to:400,,,Strongyloides ratti,,,,,1289830,,SriL3_66K_212889,Strongyloides ratti,Strongyloides_ratti (20100601),,,,1,0,0,Strongyloides ratti is a common gastro-intestinal parasite of the rat. The adult parasites are female only%2C about 2mm long and live in the mucosa of the small intestine. These parasites produce eggs that pass out of the host in its faeces. In the environment infective larval stages develop either directly or after a facultative sexual free-living adult generation. Infective larvae infect hosts by skin penetration.%0A%0AS. ratti is the laboratory analogue of the parasite of humans%2C S. stercoralis. S. stercoralis is a wide-spread parasite of humans%2C occurring principally in the tropics and sub-tropics%3A some 100-200 million people are infected worldwide. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis%2C in which worms occur throughout the body. This can be fatal unless anti-Strongyloides therapy is given. Other species of Strongyloides parasitise a wide range of vertebrates. %0A%0AAs part of the Strongyloides ratti genome project we are profiling the transcriptome of the parasite across its life cycle using RNA-Seq.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria)%2C please see http%3A%2F%2Fwww.sanger.ac.uk%2Fdatasharing%2F,521,Strongyloides ratti transcriptomics,,,Transcriptome sequencing of Strongyloides ratti,, +3789277,ERS092590,,,qPCR only,,,,,,,,0,0,3911772,0,3789277,Strongyloides ratti,34506,S0702,,,standard,,,from:300 to:400,ERS092590,,Strongyloides ratti,0,,,,1289830,,SriL3_66K_212889,Strongyloides ratti,Strongyloides_ratti (20100601),,,ERP001672,1,0,0,Strongyloides ratti is a common gastro-intestinal parasite of the rat.,521,Strongyloides ratti transcriptomics, ,0,Transcriptome sequencing of Strongyloides ratti,, diff --git a/t/data/samplesheet/dual_index_default_new.csv b/t/data/samplesheet/dual_index_default_new.csv new file mode 100644 index 00000000..fc4e4ec3 --- /dev/null +++ b/t/data/samplesheet/dual_index_default_new.csv @@ -0,0 +1,50 @@ +[Header],,,, +Investigator Name,mq1,,, +Project Name,ImmunoAgeing_Colonies_WGS,,, +Experiment Name,6946,,, +Date,2011-10-14T16:32:00,,, +Workflow,GenerateFASTQ,,, +Chemistry,Amplicon,,, +,,,, +[Reads],,,, +151,,,, +151,,,, +,,,, +[Settings],,,, +,,,, +[Manifests],,,, +,,,, +[Data],,,, +Sample_ID,Sample_Name,GenomeFolder,Index,Index2, +27037064,EGAN00002490956,,CGTGACAC,TTATTGCG, +27037100,EGAN00002490958,,ACTTAGAG,CTCCATAA, +27037112,EGAN00002490960,,TCAGGAAA,CCAAACCC, +27037089,EGAN00002490966,,CGTCACCA,CTTGTTAA, +27037101,EGAN00002490967,,GTGTTTCT,AAAGTGCG, +27037113,EGAN00002490968,,GGCACTCA,AAGTACAG, +27037125,EGAN00002490970,,GTCATCTT,GCGCGCTA, +27037090,EGAN00002490973,,AGAGCTTA,TATAAAGC, +27037114,EGAN00002490976,,CTAAGTCC,TATCAAAG, +27037091,EGAN00002490982,,GATCTTGA,GTCCCGCA, +27037056,EGAN00002491016,,GCGACTGA,CGCTTCAC, +27037104,EGAN00002491020,,TCCGGATT,CACAAGGA, +27037129,EGAN00002491021,,AACGACTG,GAAATTAT, +27037105,EGAN00002491029,,CTCGTGTC,TAGAGATA, +27037117,EGAN00002491028,,TGGCGGTC,AGCGTATT, +27037058,EGAN00002491033,,TGATTTCC,ACTTCCGA, +27037094,EGAN00002491035,,TTTAAATG,ACGTTTAA, +27037106,EGAN00002491037,,ACCTGCGG,ACGCCGCG, +27037047,EGAN00002491039,,GACCGCAG,GGTCCCTC, +27037071,EGAN00002491041,,GTTTCATG,CAAACAAA, +27037083,EGAN00002491042,,AAACATCG,ACCAAAGC, +27037048,EGAN00002491047,,GCTGCGCT,CCGATAAA, +27037072,EGAN00002491048,,TGTCAGCT,CGCCGCCC, +27037084,EGAN00002490985,,CTCTCCGG,TGCCGGCA, +27037134,EGAN00002490989,,AGAGTTAC,GATGGCTA, +27037061,EGAN00002490991,,CTCTTTAT,AAGCTCCG, +27037073,EGAN00002490992,,AGAGAGCC,ATAGGCAA, +27037085,EGAN00002490993,,CATCCACT,CCGGTGCC, +27037086,EGAN00002491001,,CATTCTTC,TAACCGCG, +27037098,EGAN00002491002,,CTCGACGT,GAAGAGCC, +27037110,EGAN00002491003,,AGTTGCAA,ATCCTGAG, +27037051,EGAN00002491009,,GTAAGATG,AAAGGCTG, diff --git a/t/data/samplesheet/dual_index_extended_new.csv b/t/data/samplesheet/dual_index_extended_new.csv new file mode 100644 index 00000000..aa3e3f8c --- /dev/null +++ b/t/data/samplesheet/dual_index_extended_new.csv @@ -0,0 +1,34 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +27037064,EGAN00002490956,,CGTGACAC,TTATTGCG,,Standard,CGTGACAC,TTATTGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037064,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490956,Normal,Homo sapiens,0,,,PD41305k_99,4396647,,6133STDY8786628,PD41305k_99,,PD41305k_99,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,1, +27037100,EGAN00002490958,,ACTTAGAG,CTCCATAA,,Standard,ACTTAGAG,CTCCATAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037100,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490958,Normal,Homo sapiens,0,,,PD41305k_102,4396650,,6133STDY8786631,PD41305k_102,,PD41305k_102,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,2, +27037112,EGAN00002490960,,TCAGGAAA,CCAAACCC,,Standard,TCAGGAAA,CCAAACCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037112,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490960,Normal,Homo sapiens,0,,,PD41305k_103,4396651,,6133STDY8786632,PD41305k_103,,PD41305k_103,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,3, +27037089,EGAN00002490966,,CGTCACCA,CTTGTTAA,,Standard,CGTCACCA,CTTGTTAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037089,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490966,Normal,Homo sapiens,0,,,PD41305k_109,4396657,,6133STDY8786638,PD41305k_109,,PD41305k_109,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,4, +27037101,EGAN00002490967,,GTGTTTCT,AAAGTGCG,,Standard,GTGTTTCT,AAAGTGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037101,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490967,Normal,Homo sapiens,0,,,PD41305k_110,4396658,,6133STDY8786639,PD41305k_110,,PD41305k_110,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,5, +27037113,EGAN00002490968,,GGCACTCA,AAGTACAG,,Standard,GGCACTCA,AAGTACAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037113,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490968,Normal,Homo sapiens,0,,,PD41305k_111,4396659,,6133STDY8786640,PD41305k_111,,PD41305k_111,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,6, +27037125,EGAN00002490970,,GTCATCTT,GCGCGCTA,,Standard,GTCATCTT,GCGCGCTA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037125,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490970,Normal,Homo sapiens,0,,,PD41305k_112,4396660,,6133STDY8786641,PD41305k_112,,PD41305k_112,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,7, +27037090,EGAN00002490973,,AGAGCTTA,TATAAAGC,,Standard,AGAGCTTA,TATAAAGC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037090,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490973,Normal,Homo sapiens,0,,,PD41305k_117,4396665,,6133STDY8786646,PD41305k_117,,PD41305k_117,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,8, +27037114,EGAN00002490976,,CTAAGTCC,TATCAAAG,,Standard,CTAAGTCC,TATCAAAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037114,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490976,Normal,Homo sapiens,0,,,PD41305k_119,4396667,,6133STDY8786648,PD41305k_119,,PD41305k_119,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,9, +27037091,EGAN00002490982,,GATCTTGA,GTCCCGCA,,Standard,GATCTTGA,GTCCCGCA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037091,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490982,Normal,Homo sapiens,0,,,PD41305k_125,4396673,,6133STDY8786654,PD41305k_125,,PD41305k_125,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,10, +27037056,EGAN00002491016,,GCGACTGA,CGCTTCAC,,Standard,GCGACTGA,CGCTTCAC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037056,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491016,Normal,Homo sapiens,0,,,PD41305k_130,4396678,,6133STDY8786659,PD41305k_130,,PD41305k_130,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,11, +27037104,EGAN00002491020,,TCCGGATT,CACAAGGA,,Standard,TCCGGATT,CACAAGGA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037104,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491020,Normal,Homo sapiens,0,,,PD41305k_134,4396682,,6133STDY8786663,PD41305k_134,,PD41305k_134,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,12, +27037129,EGAN00002491021,,AACGACTG,GAAATTAT,,Standard,AACGACTG,GAAATTAT,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037129,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491021,Normal,Homo sapiens,0,,,PD41305k_136,4396684,,6133STDY8786665,PD41305k_136,,PD41305k_136,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,13, +27037105,EGAN00002491029,,CTCGTGTC,TAGAGATA,,Standard,CTCGTGTC,TAGAGATA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037105,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491029,Normal,Homo sapiens,0,,,PD41305k_142,4396690,,6133STDY8786671,PD41305k_142,,PD41305k_142,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,14, +27037117,EGAN00002491028,,TGGCGGTC,AGCGTATT,,Standard,TGGCGGTC,AGCGTATT,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037117,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491028,Normal,Homo sapiens,0,,,PD41305k_143,4396691,,6133STDY8786672,PD41305k_143,,PD41305k_143,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,15, +27037058,EGAN00002491033,,TGATTTCC,ACTTCCGA,,Standard,TGATTTCC,ACTTCCGA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037058,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491033,Normal,Homo sapiens,0,,,PD41305k_146,4396694,,6133STDY8786675,PD41305k_146,,PD41305k_146,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,16, +27037094,EGAN00002491035,,TTTAAATG,ACGTTTAA,,Standard,TTTAAATG,ACGTTTAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037094,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491035,Normal,Homo sapiens,0,,,PD41305k_149,4396697,,6133STDY8786678,PD41305k_149,,PD41305k_149,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,17, +27037106,EGAN00002491037,,ACCTGCGG,ACGCCGCG,,Standard,ACCTGCGG,ACGCCGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037106,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491037,Normal,Homo sapiens,0,,,PD41305k_150,4396698,,6133STDY8786679,PD41305k_150,,PD41305k_150,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,18, +27037047,EGAN00002491039,,GACCGCAG,GGTCCCTC,,Standard,GACCGCAG,GGTCCCTC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037047,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491039,Normal,Homo sapiens,0,,,PD41305k_153,4396701,,6133STDY8786682,PD41305k_153,,PD41305k_153,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,19, +27037071,EGAN00002491041,,GTTTCATG,CAAACAAA,,Standard,GTTTCATG,CAAACAAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037071,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491041,Normal,Homo sapiens,0,,,PD41305k_155,4396703,,6133STDY8786684,PD41305k_155,,PD41305k_155,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,20, +27037083,EGAN00002491042,,AAACATCG,ACCAAAGC,,Standard,AAACATCG,ACCAAAGC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037083,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491042,Normal,Homo sapiens,0,,,PD41305k_156,4396704,,6133STDY8786685,PD41305k_156,,PD41305k_156,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,21, +27037048,EGAN00002491047,,GCTGCGCT,CCGATAAA,,Standard,GCTGCGCT,CCGATAAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037048,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491047,Normal,Homo sapiens,0,,,PD41305k_161,4396709,,6133STDY8786690,PD41305k_161,,PD41305k_161,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,22, +27037072,EGAN00002491048,,TGTCAGCT,CGCCGCCC,,Standard,TGTCAGCT,CGCCGCCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037072,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491048,Normal,Homo sapiens,0,,,PD41305k_163,4396711,,6133STDY8786692,PD41305k_163,,PD41305k_163,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,23, +27037084,EGAN00002490985,,CTCTCCGG,TGCCGGCA,,Standard,CTCTCCGG,TGCCGGCA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037084,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490985,Normal,Homo sapiens,0,,,PD41305k_164,4396712,,6133STDY8786693,PD41305k_164,,PD41305k_164,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,24, +27037134,EGAN00002490989,,AGAGTTAC,GATGGCTA,,Standard,AGAGTTAC,GATGGCTA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037134,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490989,Normal,Homo sapiens,0,,,PD41305k_168,4396716,,6133STDY8786697,PD41305k_168,,PD41305k_168,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,25, +27037061,EGAN00002490991,,CTCTTTAT,AAGCTCCG,,Standard,CTCTTTAT,AAGCTCCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037061,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490991,Normal,Homo sapiens,0,,,PD41305k_170,4396718,,6133STDY8786699,PD41305k_170,,PD41305k_170,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,26, +27037073,EGAN00002490992,,AGAGAGCC,ATAGGCAA,,Standard,AGAGAGCC,ATAGGCAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037073,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490992,Normal,Homo sapiens,0,,,PD41305k_171,4396719,,6133STDY8786700,PD41305k_171,,PD41305k_171,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,27, +27037085,EGAN00002490993,,CATCCACT,CCGGTGCC,,Standard,CATCCACT,CCGGTGCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037085,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490993,Normal,Homo sapiens,0,,,PD41305k_172,4396720,,6133STDY8786701,PD41305k_172,,PD41305k_172,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,28, +27037086,EGAN00002491001,,CATTCTTC,TAACCGCG,,Standard,CATTCTTC,TAACCGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037086,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491001,Normal,Homo sapiens,0,,,PD41305k_180,4396728,,6133STDY8786709,PD41305k_180,,PD41305k_180,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,29, +27037098,EGAN00002491002,,CTCGACGT,GAAGAGCC,,Standard,CTCGACGT,GAAGAGCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037098,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491002,Normal,Homo sapiens,0,,,PD41305k_181,4396729,,6133STDY8786710,PD41305k_181,,PD41305k_181,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,30, +27037110,EGAN00002491003,,AGTTGCAA,ATCCTGAG,,Standard,AGTTGCAA,ATCCTGAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037110,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491003,Normal,Homo sapiens,0,,,PD41305k_182,4396730,,6133STDY8786711,PD41305k_182,,PD41305k_182,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,31, +27037051,EGAN00002491009,,GTAAGATG,AAAGGCTG,,Standard,GTAAGATG,AAAGGCTG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037051,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491009,Normal,Homo sapiens,0,,,PD41305k_185,4396733,,6133STDY8786714,PD41305k_185,,PD41305k_185,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,32, diff --git a/t/data/samplesheet/st/batches/1.xml b/t/data/samplesheet/st/batches/1.xml deleted file mode 100644 index ef9c612d..00000000 --- a/t/data/samplesheet/st/batches/1.xml +++ /dev/null @@ -1,87 +0,0 @@ - - - 1 - released - - - - - - 1 - CGATGTTT - 6 - - - AAAAAAAA - 86 - - - - - - 2 - TTAGGCAT - 6 - - - AAAAAAAA - 86 - - - - - - 3 - TGACCACT - 6 - - - AAAAAAAA - 86 - - - - - - - - - - 374 - GCTAACTC - 6 - - - GGGGGGGG - 86 - - - - - - 375 - GATTCATC - 6 - - - GGGGGGGG - 86 - - - - - - 376 - GTCTTGGC - 6 - - - GGGGGGGG - 86 - - - - - - - diff --git a/t/data/samplesheet/st/batches/13994.xml b/t/data/samplesheet/st/batches/13994.xml deleted file mode 100644 index 30f7c51c..00000000 --- a/t/data/samplesheet/st/batches/13994.xml +++ /dev/null @@ -1,107 +0,0 @@ - - - 13994 - released - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - - diff --git a/t/data/samplesheet/st/batches/14505.xml b/t/data/samplesheet/st/batches/14505.xml deleted file mode 100644 index 1a86f0a4..00000000 --- a/t/data/samplesheet/st/batches/14505.xml +++ /dev/null @@ -1,14 +0,0 @@ - - - 14505 - released - - - - - - - - - - diff --git a/t/data/samplesheet/st/batches/16537.xml b/t/data/samplesheet/st/batches/16537.xml deleted file mode 100644 index 55e97b23..00000000 --- a/t/data/samplesheet/st/batches/16537.xml +++ /dev/null @@ -1,51 +0,0 @@ - - - 16537 - released - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - - diff --git a/t/data/samplesheet/st/batches/16538.xml b/t/data/samplesheet/st/batches/16538.xml deleted file mode 100755 index 974867a5..00000000 --- a/t/data/samplesheet/st/batches/16538.xml +++ /dev/null @@ -1,51 +0,0 @@ - - - 16537 - released - - - - - - 1 - ATCACGTTATAAAAAA - 7 - - - - - - 2 - CGATGTTTATTTTTTT - 7 - - - - - - 8 - ACTTGATGATCCCCCC - 7 - - - - - - 9 - GATCAGCGATGGGGGG - 7 - - - - - - 10 - TAGCTTGTATACACGT - 7 - - - - - - - diff --git a/t/data/samplesheet/st/batches/23798.xml b/t/data/samplesheet/st/batches/23798.xml deleted file mode 100644 index 3b0c0979..00000000 --- a/t/data/samplesheet/st/batches/23798.xml +++ /dev/null @@ -1,939 +0,0 @@ - - - 23798 - started - - - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - TAAGGCGATAGATCGC - 24 - - - - - - 2 - CGTACTAGTAGATCGC - 24 - - - - - - 3 - AGGCAGAATAGATCGC - 24 - - - - - - 4 - TCCTGAGCTAGATCGC - 24 - - - - - - 5 - GGACTCCTTAGATCGC - 24 - - - - - - 6 - TAGGCATGTAGATCGC - 24 - - - - - - 7 - CTCTCTACTAGATCGC - 24 - - - - - - 8 - CAGAGAGGTAGATCGC - 24 - - - - - - 9 - GCTACGCTTAGATCGC - 24 - - - - - - 10 - CGAGGCTGTAGATCGC - 24 - - - - - - 11 - AAGAGGCATAGATCGC - 24 - - - - - - 12 - GTAGAGGATAGATCGC - 24 - - - - - - 13 - TAAGGCGACTCTCTAT - 24 - - - - - - 14 - CGTACTAGCTCTCTAT - 24 - - - - - - 15 - AGGCAGAACTCTCTAT - 24 - - - - - - 16 - TCCTGAGCCTCTCTAT - 24 - - - - - - 17 - GGACTCCTCTCTCTAT - 24 - - - - - - 18 - TAGGCATGCTCTCTAT - 24 - - - - - - 19 - CTCTCTACCTCTCTAT - 24 - - - - - - 20 - CAGAGAGGCTCTCTAT - 24 - - - - - - 21 - 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Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 590 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Salmonella_pullorum (449_87) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289833.xml b/t/data/samplesheet/st/samples/1289833.xml deleted file mode 100644 index 63245862..00000000 --- a/t/data/samplesheet/st/samples/1289833.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289833 - bp200shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - Bpst24 - - - Organism - Bordetella Pertussis - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Bordetella Pertussis - - - Public Name - Bordetella Pertussis - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - High GC - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 520 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Bordetella_pertussis (ST24) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289834.xml b/t/data/samplesheet/st/samples/1289834.xml deleted file mode 100644 index 4013d67b..00000000 --- a/t/data/samplesheet/st/samples/1289834.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289834 - 3D7200shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - 3D7 - - - Organism - Plasmodium Falciparum - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Plasmodium Falciparum - - - Public Name - Plasmodium Falciparum - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - High AT - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 5820 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289835.xml b/t/data/samplesheet/st/samples/1289835.xml deleted file mode 100644 index 696b1f95..00000000 --- a/t/data/samplesheet/st/samples/1289835.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289835 - human200shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - colo_829 - - - Organism - Homo sapiens - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Human - - - Public Name - Homo sapiens - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - Neutral - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 9606 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Homo_sapiens (GRCh37_53) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289836.xml b/t/data/samplesheet/st/samples/1289836.xml deleted file mode 100644 index 2bd26c29..00000000 --- a/t/data/samplesheet/st/samples/1289836.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289836 - sp300shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - 449_87 - - - Organism - Salmonella pullorum - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Salmonella pullorum - - - Public Name - Salmonella pullorum - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - Neutral - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 590 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Salmonella_pullorum (449_87) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289837.xml b/t/data/samplesheet/st/samples/1289837.xml deleted file mode 100644 index cf753bed..00000000 --- a/t/data/samplesheet/st/samples/1289837.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289837 - bp300shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - Bpst24 - - - Organism - Bordetella Pertussis - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Bordetella Pertussis - - - Public Name - Bordetella Pertussis - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - High GC - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 520 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Bordetella_pertussis (ST24) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289838.xml b/t/data/samplesheet/st/samples/1289838.xml deleted file mode 100644 index 2bd2afda..00000000 --- a/t/data/samplesheet/st/samples/1289838.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289838 - 3D7300shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - 3D7 - - - Organism - Plasmodium Falciparum - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Plasmodium Falciparum - - - Public Name - Plasmodium Falciparum - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - High AT - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 5820 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289839.xml b/t/data/samplesheet/st/samples/1289839.xml deleted file mode 100644 index 5a62b2f5..00000000 --- a/t/data/samplesheet/st/samples/1289839.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289839 - human300shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - colo_829 - - - Organism - Homo sapiens - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Human - - - Public Name - Homo sapiens - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - Neutral - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 9606 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Homo_sapiens (GRCh37_53) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289840.xml b/t/data/samplesheet/st/samples/1289840.xml deleted file mode 100644 index 3242ca79..00000000 --- a/t/data/samplesheet/st/samples/1289840.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289840 - sp400shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - 449_87 - - - Organism - Salmonella pullorum - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Salmonella pullorum - - - Public Name - Salmonella pullorum - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - Neutral - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 590 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Salmonella_pullorum (449_87) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289841.xml b/t/data/samplesheet/st/samples/1289841.xml deleted file mode 100644 index ba26d759..00000000 --- a/t/data/samplesheet/st/samples/1289841.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289841 - bp400shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - Bpst24 - - - Organism - Bordetella Pertussis - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Bordetella Pertussis - - - Public Name - Bordetella Pertussis - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - High GC - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 520 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Bordetella_pertussis (ST24) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289842.xml b/t/data/samplesheet/st/samples/1289842.xml deleted file mode 100644 index 03e055f0..00000000 --- a/t/data/samplesheet/st/samples/1289842.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289842 - 3D7400shear - 700 - - - Age - - - - Ethnicity - - - - Subject - - - - Genotype - - - - Purification method - - - - Sample extraction method - - - - Sibling - - - - Sample Visibility - Hold - - - Sample Description - genomic DNA - - - Disease - - - - Sample type - - - - Time Point - - - - RNAi - - - - Compound - - - - Volume (µl) - - - - Sample storage conditions - - - - ENA Sample Accession Number - - - - Strain - 3D7 - - - Organism - Plasmodium Falciparum - - - Treatment - - - - Growth Condition - - - - Immunoprecipitate - - - - Dose - - - - Is re-submitted? - - - - Country of origin - - - - Organism Part - - - - Sample purified - - - - Date of sample extraction - - - - Common Name - Plasmodium Falciparum - - - Public Name - Plasmodium Falciparum - - - DNA source - Genomic - - - Mother - - - - Concentration determind by - - - - Gender - - - - GC content - High AT - - - Father - - - - Plate - - - - Disease State - - - - Developmental Stage - - - - Date of sample collection - - - - TAXON ID - 5820 - - - Replicate - - - - Cell Type - - - - Phenotype - - - - Concentration - - - - Geographical region - - - - Cohort - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1289843.xml b/t/data/samplesheet/st/samples/1289843.xml deleted file mode 100644 index d69233c9..00000000 --- a/t/data/samplesheet/st/samples/1289843.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1289843 - human400shear - 700 - - - Phenotype - - - - Sample purified - - - - TAXON ID - 9606 - - - Country of origin - - - - Treatment - - - - Time Point - - - - Date of sample extraction - - - - Sample Description - genomic DNA - - - ENA Sample Accession Number - - - - Common Name - Human - - - Gender - - - - Mother - - - - Ethnicity - - - - Compound - - - - Cell Type - - - - Age - - - - Genotype - - - - Volume (µl) - - - - Dose - - - - Organism Part - - - - Growth Condition - - - - Concentration - - - - Public Name - Homo sapiens - - - Subject - - - - RNAi - - - - Concentration determind by - - - - Is re-submitted? - - - - DNA source - Genomic - - - Sample extraction method - - - - Disease - - - - Sibling - - - - Strain - colo_829 - - - Cohort - - - - Immunoprecipitate - - - - Disease State - - - - Sample storage conditions - - - - Sample type - - - - Date of sample collection - - - - Developmental Stage - - - - Purification method - - - - Sample Visibility - Hold - - - GC content - Neutral - - - Father - - - - Plate - - - - Geographical region - - - - Replicate - - - - Organism - Homo sapiens - - - Reference Genome - Homo_sapiens (GRCh37_53) - - - - - - - - - 700 - diff --git a/t/data/samplesheet/st/samples/1392234.xml b/t/data/samplesheet/st/samples/1392234.xml deleted file mode 100644 index 4bb1eac1..00000000 --- a/t/data/samplesheet/st/samples/1392234.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1392234 - PfIT_Sanger_5kb - 1980 - - - Age - - - - Sample Description - - - - Common Name - - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - - - - Strain - - - - GC content - High AT - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 1980 - diff --git a/t/data/samplesheet/st/samples/1392235.xml b/t/data/samplesheet/st/samples/1392235.xml deleted file mode 100644 index c9b644f1..00000000 --- a/t/data/samplesheet/st/samples/1392235.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1392235 - PfIT_SOLiD5500_5kb - 1980 - - - Age - - - - Sample Description - - - - Common Name - - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - - - - Strain - - - - GC content - High AT - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 1980 - diff --git a/t/data/samplesheet/st/samples/1392236.xml b/t/data/samplesheet/st/samples/1392236.xml deleted file mode 100644 index f2c05406..00000000 --- a/t/data/samplesheet/st/samples/1392236.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1392236 - PfIT_454_5kb - 1980 - - - Age - - - - Sample Description - - - - Common Name - - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - - - - Strain - - - - GC content - High AT - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 1980 - diff --git a/t/data/samplesheet/st/samples/1392237.xml b/t/data/samplesheet/st/samples/1392237.xml deleted file mode 100644 index 10f04721..00000000 --- a/t/data/samplesheet/st/samples/1392237.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1392237 - Tetse_3kb - 1980 - - - Age - - - - Sample Description - - - - Common Name - - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - - - - Strain - - - - GC content - High AT - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Reference Genome - - - - - - - - - - 1980 - diff --git a/t/data/samplesheet/st/samples/1392238.xml b/t/data/samplesheet/st/samples/1392238.xml deleted file mode 100644 index 02b0c91a..00000000 --- a/t/data/samplesheet/st/samples/1392238.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 1392238 - Mouse_test_3kb - 1980 - - - Age - - - - Sample Description - - - - Common Name - - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - - - - Strain - - - - GC content - Neutral - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 1980 - diff --git a/t/data/samplesheet/st/samples/1660679.xml b/t/data/samplesheet/st/samples/1660679.xml deleted file mode 100644 index b1cef7fb..00000000 --- a/t/data/samplesheet/st/samples/1660679.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1660679 - Hc_4_BC4_P2_5046_340285 - 1697 - false - - - Organism - Haemonchus contortus - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Mixed - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Haemonchus contortus MHco3/4.BC4(P2)-5046 - - - Common Name - Haemonchus contortus - - - Strain - MHco3/4.BC4(P2)-5046 - - - TAXON ID - 6289 - - - ENA Sample Accession Number - ERS323818 - - - Sample Description - 25-30 mixed male and female worms, strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - Haemonchus_contortus (V1_21June13) - - - - - - - - 1697 - diff --git a/t/data/samplesheet/st/samples/1660680.xml b/t/data/samplesheet/st/samples/1660680.xml deleted file mode 100644 index 9722cc04..00000000 --- a/t/data/samplesheet/st/samples/1660680.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1660680 - Hc_10_BC4_P2_5779_340285 - 1697 - false - - - Organism - Haemonchus contortus - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Mixed - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Haemonchus contortus MHco3/10.BC4(P2)-5779 - - - Common Name - Haemonchus contortus - - - Strain - MHco3/10.BC4(P2)-5779 - - - TAXON ID - 6289 - - - ENA Sample Accession Number - ERS323819 - - - Sample Description - 25-30 mixed male and female worms, strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - Haemonchus_contortus (V1_21June13) - - - - - - - - 1697 - diff --git a/t/data/samplesheet/st/samples/1694494.xml b/t/data/samplesheet/st/samples/1694494.xml deleted file mode 100644 index 5b19be0e..00000000 --- a/t/data/samplesheet/st/samples/1694494.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1694494 - T_BCM1_F4 - 2501 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - RT_37 - - - Common Name - Mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS354532 - - - Sample Description - RNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - 8 weeks - - - Developmental Stage - N/A - - - Cell Type - T cells - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - - - - - - - - - - 2501 - diff --git a/t/data/samplesheet/st/samples/1694495.xml b/t/data/samplesheet/st/samples/1694495.xml deleted file mode 100644 index 09c98a30..00000000 --- a/t/data/samplesheet/st/samples/1694495.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1694495 - T_BCM1_F5 - 2501 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - RT_38 - - - Common Name - Mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS354533 - - - Sample Description - RNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - 8 weeks - - - Developmental Stage - N/A - - - Cell Type - T cells - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - - - - - - - - - - 2501 - diff --git a/t/data/samplesheet/st/samples/1694496.xml b/t/data/samplesheet/st/samples/1694496.xml deleted file mode 100644 index e81e3ea0..00000000 --- a/t/data/samplesheet/st/samples/1694496.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1694496 - T_CBF1_G4 - 2501 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - RT_39 - - - Common Name - Mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS354534 - - - Sample Description - RNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - 8 weeks - - - Developmental Stage - N/A - - - Cell Type - T cells - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - - - - - - - - - - 2501 - diff --git a/t/data/samplesheet/st/samples/1694497.xml b/t/data/samplesheet/st/samples/1694497.xml deleted file mode 100644 index 8e75af7a..00000000 --- a/t/data/samplesheet/st/samples/1694497.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1694497 - T_CBF1_G5 - 2501 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - RT_40 - - - Common Name - Mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS354535 - - - Sample Description - RNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - 8 weeks - - - Developmental Stage - N/A - - - Cell Type - T cells - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - - - - - - - - - - 2501 - diff --git a/t/data/samplesheet/st/samples/1694498.xml b/t/data/samplesheet/st/samples/1694498.xml deleted file mode 100644 index 25743f1e..00000000 --- a/t/data/samplesheet/st/samples/1694498.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1694498 - T_CBM2_H4 - 2501 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - RT_41 - - - Common Name - Mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS354536 - - - Sample Description - RNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - 8 weeks - - - Developmental Stage - N/A - - - Cell Type - T cells - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - - - - - - - - - - 2501 - diff --git a/t/data/samplesheet/st/samples/1694499.xml b/t/data/samplesheet/st/samples/1694499.xml deleted file mode 100644 index 826bec8c..00000000 --- a/t/data/samplesheet/st/samples/1694499.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1694499 - T_CBM2_H5 - 2501 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - RT_42 - - - Common Name - Mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS354537 - - - Sample Description - RNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - 8 weeks - - - Developmental Stage - N/A - - - Cell Type - T cells - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - - - - - - - - - - 2501 - diff --git a/t/data/samplesheet/st/samples/1706390.xml b/t/data/samplesheet/st/samples/1706390.xml deleted file mode 100644 index 187d5307..00000000 --- a/t/data/samplesheet/st/samples/1706390.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706390 - mES_ai2_s2_cell1 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 1 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell1 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351213 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706391.xml b/t/data/samplesheet/st/samples/1706391.xml deleted file mode 100644 index 8b187d5e..00000000 --- a/t/data/samplesheet/st/samples/1706391.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706391 - mES_ai2_s2_cell2 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 2 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell2 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351214 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706392.xml b/t/data/samplesheet/st/samples/1706392.xml deleted file mode 100644 index 9b0cdbd3..00000000 --- a/t/data/samplesheet/st/samples/1706392.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706392 - mES_ai2_s2_cell3 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 3 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell3 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351221 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706393.xml b/t/data/samplesheet/st/samples/1706393.xml deleted file mode 100644 index 34a5f3e2..00000000 --- a/t/data/samplesheet/st/samples/1706393.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706393 - mES_ai2_s2_cell4 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 4 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell4 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351222 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706394.xml b/t/data/samplesheet/st/samples/1706394.xml deleted file mode 100644 index bb2f4e57..00000000 --- a/t/data/samplesheet/st/samples/1706394.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706394 - mES_ai2_s2_cell5 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 5 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell5 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351223 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706395.xml b/t/data/samplesheet/st/samples/1706395.xml deleted file mode 100644 index 8d9130d0..00000000 --- a/t/data/samplesheet/st/samples/1706395.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706395 - mES_ai2_s2_cell6 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 6 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell6 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351224 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706396.xml b/t/data/samplesheet/st/samples/1706396.xml deleted file mode 100644 index 4b36b579..00000000 --- a/t/data/samplesheet/st/samples/1706396.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706396 - mES_ai2_s2_cell7 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 7 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell7 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351225 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706397.xml b/t/data/samplesheet/st/samples/1706397.xml deleted file mode 100644 index a75b66e9..00000000 --- a/t/data/samplesheet/st/samples/1706397.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706397 - mES_ai2_s2_cell8 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 8 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell8 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351218 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706398.xml b/t/data/samplesheet/st/samples/1706398.xml deleted file mode 100644 index 0759aeac..00000000 --- a/t/data/samplesheet/st/samples/1706398.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706398 - mES_ai2_s2_cell9 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 9 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell9 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351219 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706399.xml b/t/data/samplesheet/st/samples/1706399.xml deleted file mode 100644 index 93bf42c7..00000000 --- a/t/data/samplesheet/st/samples/1706399.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706399 - mES_ai2_s2_cell10 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 10 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell10 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351220 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706400.xml b/t/data/samplesheet/st/samples/1706400.xml deleted file mode 100644 index 5308e0e6..00000000 --- a/t/data/samplesheet/st/samples/1706400.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706400 - mES_ai2_s2_cell11 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 11 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell11 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351235 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706401.xml b/t/data/samplesheet/st/samples/1706401.xml deleted file mode 100644 index 2d8e7b64..00000000 --- a/t/data/samplesheet/st/samples/1706401.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706401 - mES_ai2_s2_cell12 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 12 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell12 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351237 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706402.xml b/t/data/samplesheet/st/samples/1706402.xml deleted file mode 100644 index fe3fa615..00000000 --- a/t/data/samplesheet/st/samples/1706402.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706402 - mES_ai2_s2_cell13 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 13 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell13 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351238 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706403.xml b/t/data/samplesheet/st/samples/1706403.xml deleted file mode 100644 index 179f6da4..00000000 --- a/t/data/samplesheet/st/samples/1706403.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706403 - mES_ai2_s2_cell14 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 14 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell14 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351239 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706404.xml b/t/data/samplesheet/st/samples/1706404.xml deleted file mode 100644 index 47acebe5..00000000 --- a/t/data/samplesheet/st/samples/1706404.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706404 - mES_ai2_s2_cell15 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 15 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell15 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351241 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706405.xml b/t/data/samplesheet/st/samples/1706405.xml deleted file mode 100644 index ffeabda5..00000000 --- a/t/data/samplesheet/st/samples/1706405.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706405 - mES_ai2_s2_cell16 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 16 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell16 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351226 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706406.xml b/t/data/samplesheet/st/samples/1706406.xml deleted file mode 100644 index 3b3d8653..00000000 --- a/t/data/samplesheet/st/samples/1706406.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706406 - mES_ai2_s2_cell17 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 17 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell17 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351227 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706407.xml b/t/data/samplesheet/st/samples/1706407.xml deleted file mode 100644 index 528716e1..00000000 --- a/t/data/samplesheet/st/samples/1706407.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706407 - mES_ai2_s2_cell18 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 18 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell18 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351234 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706408.xml b/t/data/samplesheet/st/samples/1706408.xml deleted file mode 100644 index 5009b1b1..00000000 --- a/t/data/samplesheet/st/samples/1706408.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706408 - mES_ai2_s2_cell19 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 19 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell19 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351236 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706409.xml b/t/data/samplesheet/st/samples/1706409.xml deleted file mode 100644 index 03e3c89e..00000000 --- a/t/data/samplesheet/st/samples/1706409.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706409 - mES_ai2_s2_cell20 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 20 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell20 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351247 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706410.xml b/t/data/samplesheet/st/samples/1706410.xml deleted file mode 100644 index 0134c889..00000000 --- a/t/data/samplesheet/st/samples/1706410.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706410 - mES_ai2_s2_cell21 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 21 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell21 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351249 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706411.xml b/t/data/samplesheet/st/samples/1706411.xml deleted file mode 100644 index 769c8431..00000000 --- a/t/data/samplesheet/st/samples/1706411.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706411 - mES_ai2_s2_cell22 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 22 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell22 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351251 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706412.xml b/t/data/samplesheet/st/samples/1706412.xml deleted file mode 100644 index fc13d974..00000000 --- a/t/data/samplesheet/st/samples/1706412.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706412 - mES_ai2_s2_cell23 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 23 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell23 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351252 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706413.xml b/t/data/samplesheet/st/samples/1706413.xml deleted file mode 100644 index a464a395..00000000 --- a/t/data/samplesheet/st/samples/1706413.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706413 - mES_ai2_s2_cell24 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 24 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell24 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351242 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706414.xml b/t/data/samplesheet/st/samples/1706414.xml deleted file mode 100644 index f200e65d..00000000 --- a/t/data/samplesheet/st/samples/1706414.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706414 - mES_ai2_s2_cell25 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 25 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell25 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351243 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706415.xml b/t/data/samplesheet/st/samples/1706415.xml deleted file mode 100644 index 5c656bcc..00000000 --- a/t/data/samplesheet/st/samples/1706415.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706415 - mES_ai2_s2_cell26 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 26 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell26 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351244 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706416.xml b/t/data/samplesheet/st/samples/1706416.xml deleted file mode 100644 index c2b364da..00000000 --- a/t/data/samplesheet/st/samples/1706416.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706416 - mES_ai2_s2_cell27 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 27 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell27 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351245 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706417.xml b/t/data/samplesheet/st/samples/1706417.xml deleted file mode 100644 index 05aee223..00000000 --- a/t/data/samplesheet/st/samples/1706417.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706417 - mES_ai2_s2_cell28 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 28 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell28 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351248 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - 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Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351250 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706419.xml b/t/data/samplesheet/st/samples/1706419.xml deleted file mode 100644 index a0d5e225..00000000 --- a/t/data/samplesheet/st/samples/1706419.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706419 - mES_ai2_s2_cell30 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 30 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell30 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351260 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706420.xml b/t/data/samplesheet/st/samples/1706420.xml deleted file mode 100644 index 98c670f0..00000000 --- a/t/data/samplesheet/st/samples/1706420.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706420 - mES_ai2_s2_cell31 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 31 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell31 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351261 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706421.xml b/t/data/samplesheet/st/samples/1706421.xml deleted file mode 100644 index 2f8138ec..00000000 --- a/t/data/samplesheet/st/samples/1706421.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706421 - mES_ai2_s2_cell32 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 32 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell32 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351254 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706422.xml b/t/data/samplesheet/st/samples/1706422.xml deleted file mode 100644 index 3330ec4a..00000000 --- a/t/data/samplesheet/st/samples/1706422.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706422 - mES_ai2_s2_cell33 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 33 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell33 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351255 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is 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a/t/data/samplesheet/st/samples/1706423.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706423 - mES_ai2_s2_cell34 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 34 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell34 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351256 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706424.xml b/t/data/samplesheet/st/samples/1706424.xml deleted file mode 100644 index d6a94d6d..00000000 --- a/t/data/samplesheet/st/samples/1706424.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706424 - mES_ai2_s2_cell35 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 35 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell35 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351257 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706425.xml b/t/data/samplesheet/st/samples/1706425.xml deleted file mode 100644 index 1f63c1a2..00000000 --- a/t/data/samplesheet/st/samples/1706425.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706425 - mES_ai2_s2_cell36 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 36 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell36 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351258 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706426.xml b/t/data/samplesheet/st/samples/1706426.xml deleted file mode 100644 index 6d40a2e1..00000000 --- a/t/data/samplesheet/st/samples/1706426.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706426 - mES_ai2_s2_cell37 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 37 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell37 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351259 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706427.xml b/t/data/samplesheet/st/samples/1706427.xml deleted file mode 100644 index 378c6d6d..00000000 --- a/t/data/samplesheet/st/samples/1706427.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706427 - mES_ai2_s2_cell38 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 38 - - - GC content - Neutral - - - Gender - Male - 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- N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706428.xml b/t/data/samplesheet/st/samples/1706428.xml deleted file mode 100644 index f5a02950..00000000 --- a/t/data/samplesheet/st/samples/1706428.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706428 - mES_ai2_s2_cell39 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 39 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell39 - - - Common Name - Mus 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alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706429.xml b/t/data/samplesheet/st/samples/1706429.xml deleted file mode 100644 index 8ee6a762..00000000 --- a/t/data/samplesheet/st/samples/1706429.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706429 - mES_ai2_s2_cell40 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 40 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell40 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351262 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706430.xml b/t/data/samplesheet/st/samples/1706430.xml deleted file mode 100644 index 01cee266..00000000 --- a/t/data/samplesheet/st/samples/1706430.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706430 - mES_ai2_s2_cell41 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 41 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell41 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351263 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706431.xml b/t/data/samplesheet/st/samples/1706431.xml deleted file mode 100644 index b50c083f..00000000 --- a/t/data/samplesheet/st/samples/1706431.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706431 - mES_ai2_s2_cell42 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 42 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell42 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351264 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706432.xml b/t/data/samplesheet/st/samples/1706432.xml deleted file mode 100644 index c36efe8f..00000000 --- a/t/data/samplesheet/st/samples/1706432.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706432 - mES_ai2_s2_cell43 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 43 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell43 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351266 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706433.xml b/t/data/samplesheet/st/samples/1706433.xml deleted file mode 100644 index b29ed642..00000000 --- a/t/data/samplesheet/st/samples/1706433.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706433 - mES_ai2_s2_cell44 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 44 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell44 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351267 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706434.xml b/t/data/samplesheet/st/samples/1706434.xml deleted file mode 100644 index e9c4cfbb..00000000 --- a/t/data/samplesheet/st/samples/1706434.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706434 - mES_ai2_s2_cell45 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 45 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell45 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351268 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706435.xml b/t/data/samplesheet/st/samples/1706435.xml deleted file mode 100644 index 2634c023..00000000 --- a/t/data/samplesheet/st/samples/1706435.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706435 - mES_ai2_s2_cell46 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 46 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell46 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351270 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706436.xml b/t/data/samplesheet/st/samples/1706436.xml deleted file mode 100644 index 0f73d7e9..00000000 --- a/t/data/samplesheet/st/samples/1706436.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706436 - mES_ai2_s2_cell47 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 47 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell47 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351272 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706437.xml b/t/data/samplesheet/st/samples/1706437.xml deleted file mode 100644 index 15ed24a3..00000000 --- a/t/data/samplesheet/st/samples/1706437.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706437 - mES_ai2_s2_cell48 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 48 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell48 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351273 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706438.xml b/t/data/samplesheet/st/samples/1706438.xml deleted file mode 100644 index 07d41562..00000000 --- a/t/data/samplesheet/st/samples/1706438.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706438 - mES_ai2_s2_cell49 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 49 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell49 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351275 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - 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a/t/data/samplesheet/st/samples/1706441.xml b/t/data/samplesheet/st/samples/1706441.xml deleted file mode 100644 index fcef99ba..00000000 --- a/t/data/samplesheet/st/samples/1706441.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706441 - mES_ai2_s2_cell52 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 52 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell52 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351279 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - 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100644 index 60f65862..00000000 --- a/t/data/samplesheet/st/samples/1706442.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706442 - mES_ai2_s2_cell53 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 53 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell53 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351280 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date 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- - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706450.xml b/t/data/samplesheet/st/samples/1706450.xml deleted file mode 100644 index fb059e6b..00000000 --- a/t/data/samplesheet/st/samples/1706450.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706450 - mES_ai2_s2_cell61 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 61 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell61 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351288 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706451.xml b/t/data/samplesheet/st/samples/1706451.xml deleted file mode 100644 index 9952af75..00000000 --- a/t/data/samplesheet/st/samples/1706451.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706451 - mES_ai2_s2_cell62 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 62 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell62 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351289 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706452.xml b/t/data/samplesheet/st/samples/1706452.xml deleted file mode 100644 index 6d98519a..00000000 --- a/t/data/samplesheet/st/samples/1706452.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706452 - mES_ai2_s2_cell63 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 63 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell63 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351290 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706453.xml b/t/data/samplesheet/st/samples/1706453.xml deleted file mode 100644 index 159cf756..00000000 --- a/t/data/samplesheet/st/samples/1706453.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706453 - mES_ai2_s2_cell64 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 64 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell64 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351283 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706454.xml b/t/data/samplesheet/st/samples/1706454.xml deleted file mode 100644 index 1dd20f84..00000000 --- a/t/data/samplesheet/st/samples/1706454.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706454 - mES_ai2_s2_cell65 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 65 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell65 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351284 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706455.xml b/t/data/samplesheet/st/samples/1706455.xml deleted file mode 100644 index db8d2ccc..00000000 --- a/t/data/samplesheet/st/samples/1706455.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706455 - mES_ai2_s2_cell66 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 66 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell66 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351292 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706456.xml b/t/data/samplesheet/st/samples/1706456.xml deleted file mode 100644 index fde3fe6a..00000000 --- a/t/data/samplesheet/st/samples/1706456.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706456 - mES_ai2_s2_cell67 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 67 - - - GC content - Neutral - - - Gender - Male - 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- N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706457.xml b/t/data/samplesheet/st/samples/1706457.xml deleted file mode 100644 index dedfeaf5..00000000 --- a/t/data/samplesheet/st/samples/1706457.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706457 - mES_ai2_s2_cell68 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 68 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell68 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351294 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706458.xml b/t/data/samplesheet/st/samples/1706458.xml deleted file mode 100644 index be6aa1c0..00000000 --- a/t/data/samplesheet/st/samples/1706458.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706458 - mES_ai2_s2_cell69 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 69 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell69 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351295 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - 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Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706460.xml b/t/data/samplesheet/st/samples/1706460.xml deleted file mode 100644 index 194e65bb..00000000 --- a/t/data/samplesheet/st/samples/1706460.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706460 - mES_ai2_s2_cell71 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 71 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell71 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351297 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706461.xml b/t/data/samplesheet/st/samples/1706461.xml deleted file mode 100644 index d2c15a91..00000000 --- a/t/data/samplesheet/st/samples/1706461.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706461 - mES_ai2_s2_cell72 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 72 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell72 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351291 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - 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a/t/data/samplesheet/st/samples/1706470.xml b/t/data/samplesheet/st/samples/1706470.xml deleted file mode 100644 index 891f8f6b..00000000 --- a/t/data/samplesheet/st/samples/1706470.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706470 - mES_ai2_s2_cell81 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 81 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell81 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351300 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - 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100644 index ec28a0dd..00000000 --- a/t/data/samplesheet/st/samples/1706471.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706471 - mES_ai2_s2_cell82 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 82 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell82 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351309 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date 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b/t/data/samplesheet/st/samples/1706480.xml deleted file mode 100644 index 1a88a1b1..00000000 --- a/t/data/samplesheet/st/samples/1706480.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706480 - mES_ai2_s2_cell91 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 91 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell91 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351316 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is 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a/t/data/samplesheet/st/samples/1706481.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706481 - mES_ai2_s2_cell92 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 92 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell92 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351317 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample 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Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 94 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell94 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351319 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706484.xml b/t/data/samplesheet/st/samples/1706484.xml deleted file mode 100644 index f71f44b1..00000000 --- a/t/data/samplesheet/st/samples/1706484.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706484 - mES_ai2_s2_cell95 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 95 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell95 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351320 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1706485.xml b/t/data/samplesheet/st/samples/1706485.xml deleted file mode 100644 index ba70ebc0..00000000 --- a/t/data/samplesheet/st/samples/1706485.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1706485 - mES_ai2_s2_cell96 - 2658 - false - - - Organism - mus musculus - - - Cohort - - - - Country of origin - N/A - - - Geographical region - N/A - - - Ethnicity - N/A - - - Volume (µl) - N/A - - - Plate - - - - Mother - 129S6/SvEvTac - - - Father - C57BL/6Ncr - - - Replicate - 96 - - - GC content - Neutral - - - Gender - Male - - - Donor Id - - - - DNA source - Cell Line - - - Public Name - mES_ai2_s2_cell96 - - - Common Name - Mus Musculus - - - Strain - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS351321 - - - Sample Description - mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - G4 ES cell line from a male blastocyst from a C57BL/6Ncr male x 129S6/SvEvTac female - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - embryonic stem cell line - - - Cell Type - ESC - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - alternative 2i/LIF - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (NCBIm37) - - - - - - - - - 2658 - diff --git a/t/data/samplesheet/st/samples/1712041.xml b/t/data/samplesheet/st/samples/1712041.xml deleted file mode 100644 index 9962fb8e..00000000 --- a/t/data/samplesheet/st/samples/1712041.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1712041 - PD14393b_wg - 2239 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD14393b - - - DNA source - Genomic - - - Public Name - PD14393b - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001173643 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - normal - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 2239 - diff --git a/t/data/samplesheet/st/studies/1697.xml b/t/data/samplesheet/st/studies/1697.xml deleted file mode 100644 index cfa8a136..00000000 --- a/t/data/samplesheet/st/studies/1697.xml +++ /dev/null @@ -1,195 +0,0 @@ - - - 1697 - Haemonchus contortus Ivermectin Resistance - true - 248 - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - jc17 - jc17@sanger.ac.uk - James Cotton - 408 - - - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - - - hr1 - hr1@sanger.ac.uk - Helen Beasley - 285 - - - - - 2010-12-07 15:59:16 +0000 - 2013-07-09 16:09:58 +0100 - - - Study description - Two H. contortus ivermectin resistance strains have been backcrossed 4 times against the susceptible genome strain. Parental strains and backcross strains will be sequenced in order to identify regions of the genome linked to ivermectin resistance-conferring loci. - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - - - - Abstract - Identification of ivermectin resistance-conferring loci by sequencing and comparing the genomes of susceptible parents, resistant parents and backcross strains. - - - Title - Haemonchus contortus Ivermectin Resistance - - - ENA Study Accession Number - ERP000430 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - No - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - open - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - false - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Whole Genome Sequencing - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Faculty Sponsor - Matthew Berriman - - - diff --git a/t/data/samplesheet/st/studies/198.xml b/t/data/samplesheet/st/studies/198.xml deleted file mode 100644 index e2ad4aad..00000000 --- a/t/data/samplesheet/st/studies/198.xml +++ /dev/null @@ -1,181 +0,0 @@ - - - 198 - Illumina Controls - true - 83 - - - hps - hps@sanger.ac.uk - Harold Swerdlow - 83 - - - - - hps - hps@sanger.ac.uk - Harold Swerdlow - 83 - - - - - 2008-11-13 13:27:48 +0000 - 2013-08-12 14:14:01 +0100 - - - Study description - None - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - - - - Abstract - - - - Title - - - - ENA Study Accession Number - - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - No - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - open - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Resequencing - - - What sort of study is this? - genotyping or cytogenetics - - - Reference Genome - - - - Faculty Sponsor - None - - - diff --git a/t/data/samplesheet/st/studies/1980.xml b/t/data/samplesheet/st/studies/1980.xml deleted file mode 100644 index 4a77b318..00000000 --- a/t/data/samplesheet/st/studies/1980.xml +++ /dev/null @@ -1,161 +0,0 @@ - - - 1980 - Mate Pair R&D - true - 519 - - - nh4 - nh4@sanger.ac.uk - Naomi Park - 519 - - - - - nh4 - nh4@sanger.ac.uk - Naomi Park - 519 - - - - - 2011-09-23 10:50:04 +0100 - 2011-09-23 11:54:53 +0100 - - - Comment regarding prevention of data release and approval - R&D - - - Alignments in BAM - true - - - Abstract - To establish a robust Mate Pair library preparation protocol - - - Study Visibility - Hold - - - SNP parent study ID - - - - Has the delay period been approved by the data sharing committee for this project? - - - - ENA Study Accession Number - - - - Number of gigabases per sample (minimum 0.15) - - - - Study description - R&D - - - Will you be using WTSI's standard access agreement? - - - - Comment regarding data release timing and approval - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - What is the data release strategy for this study? - not applicable - - - EGA DAC Accession Number - - - - How is the data release to be timed? - never - - - Study name abbreviation - MPRandD - - - Has this been approved? - Yes - - - SNP study ID - - - - Delay for - - - - What is the reason for preventing data release? - data validity - - - Reason for delaying release - - - - Do any of the samples in this study contain human DNA? - No - - - ENA Project ID - 0 - - - ArrayExpress Accession Number - - - - EGA Policy Accession Number - - - - Policy - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Title - Mate Pair R&D - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Reference Genome - - - - What sort of study is this? - genomic sequencing - - - Faculty Sponsor - Harold Swerdlow - - - Study Type - Whole Genome Sequencing - - - diff --git a/t/data/samplesheet/st/studies/2239.xml b/t/data/samplesheet/st/studies/2239.xml deleted file mode 100644 index 7332de15..00000000 --- a/t/data/samplesheet/st/studies/2239.xml +++ /dev/null @@ -1,221 +0,0 @@ - - - 2239 - MPN Whole Genomes - true - 145 - - - som - som@sanger.ac.uk - Sarah OMeara - 585 - - - las - las@sanger.ac.uk - Lucy Stebbings - 21 - - - je6 - je6@sanger.ac.uk - Jyoti Evans - 658 - - - cdt - cdt@sanger.ac.uk - Calli Latimer - 175 - - - - - sm2 - sm2@sanger.ac.uk - Stuart McLaren - 145 - - - cdt - cdt@sanger.ac.uk - Calli Latimer - 175 - - - lm5 - lm5@sanger.ac.uk - Laura Mudie - 587 - - - cs4 - cs4@sanger.ac.uk - Claire Hardy - 390 - - - - - sm2 - sm2@sanger.ac.uk - Stuart McLaren - 145 - - - - - 2012-06-08 11:15:39 +0100 - 2012-11-26 14:20:33 +0000 - - - Study description - Wholegenome libraries will be prepared from at least two serial samples reflecting different stages of disease progression and matched constitutional DNA for 30 Myeloproliferative Disease samples. Five lanes of Illumina HiSeq sequencing will be performed on each of the tumour samples and four lanes for each of the constitutional DNA. Sequencing data will mapped to build 37 of the human reference genome and analysis will be performed to characterize the spectrum of somatic variation present in these samples including single base pair mutations, insertions, deletions as well as larger structural variants and genomic rearrangements. - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - PRJEB12 - - - Abstract - Cancer is driven by mutation and is typically highly heterogeneous with each tumour represented by multiple subclonal compartments each with its unique spectrum of mutation clusters. Using whole genome library preparation and massively parallel sequencing technology, we aim to the entire genome of 30 pairs of Myeloproliferative disease samples. Bespoke algorithms are being developed to identify the somatically acquired point mutations, insertions and deletions in these samples. This project will give unprecedented insights into mutational processes, cellular repair pathways and gene networks associated with Myeloproliferative disease development and disease progression. - - - Title - Myeloproliferative Disease Whole Genomes - - - ENA Study Accession Number - EGAS00001000290 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - managed - - - Will you be using WTSI's standard access agreement? - No - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - EGAC00001000010 - - - EGA Policy Accession Number - EGAP00001000037 - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - 10/050 - - - Study Type - Cancer Genomics - - - What sort of study is this? - genomic sequencing - - - Reference Genome - Homo_sapiens (CGP_GRCh37.NCBI.allchr_MT) - - - Faculty Sponsor - Peter Campbell - - - diff --git a/t/data/samplesheet/st/studies/2501.xml b/t/data/samplesheet/st/studies/2501.xml deleted file mode 100644 index 8662a411..00000000 --- a/t/data/samplesheet/st/studies/2501.xml +++ /dev/null @@ -1,187 +0,0 @@ - - - 2501 - Mouse model to quantify genotype-epigenotype variations_RNA - true - 191 - - - ncb - ncb@sanger.ac.uk - Nathalie C Smerdon - 191 - - - - - ms27 - ms27@sanger.ac.uk - Marcela Sjoberg - 711 - - - - - 2013-01-16 13:54:59 +0000 - 2013-01-30 11:22:33 +0000 - - - Study description - In order to examine the impact of genetic variation on epigenetic marking and control of gene expression, this study has been initiated using two inbred strains of mice, C57BL/6J and CAST/Eij which genomes indicate substantial structural and nucleotide variation. Stocks of adult C57BL/6J and CAST/Eij mice as well as CAST/BL6 and BL6/CAST reciprocal hybrids are employed for isolation of pure and synchronous populations of B and T-lymphocytes. RNA-Seq expression analysis will be performed in total RNA extracted from B-lymphocytes isolated from males and females of both strains and hybrids. - -This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - - - - Abstract - Epigenetic mechanisms including non-coding RNAs are involved in the acquisition and maintenance of specific gene expression programmes during development and differentiation. Examining the extent to which DNA structural variation correlates with epigenomic and transcriptional changes is important to identify the basis of disease development, quantitative variation, adaptation and evolution. With the aim of identifying genotype-mediated epigenotype variations that account for transcriptional changes, we have used two inbred strains of mice, C57BL/6J and CAST/Eij as a model. -Pure synchronous populations of B and T-lymphocytes were isolated from males and females of both strains and reciprocal hybrids and total RNA was extracted for each sample in duplicates. Total RNA expression analysis will be performed: (1) to inspect in B lymphocytes of each strain the transcriptional programme that maintain the cellular phenotype; (2) to inspect in B lymphocytes of each strain the transcriptional programme that supress proliferation and apoptosis; (3) to look at the differential expression of various species of RNA (coding and non-coding) as a consequence of genomic variation; (3) to determine parental origin and cis/trans strain-specific effects based on the reciprocal hybrids RNA-Seq analysis. - - - - - Title - Mouse model to quantify genotype-epigenotype variations - - - ENA Study Accession Number - ERP002223 - - - Study Visibility - Public - - - Do any of the samples in this study contain human DNA? - No - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - open - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - delayed - - - Reason for delaying release - assay of no other use - - - Delay for - 12 months - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - E-ERAD-155 - - - Has the delay period been approved by the data sharing committee for this project? - Yes - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Transcriptome Analysis - - - What sort of study is this? - transcriptomics - - - Reference Genome - Mus_musculus (GRCm38) - - - Faculty Sponsor - David Adams - - - diff --git a/t/data/samplesheet/st/studies/2658.xml b/t/data/samplesheet/st/studies/2658.xml deleted file mode 100644 index 78e34ddf..00000000 --- a/t/data/samplesheet/st/studies/2658.xml +++ /dev/null @@ -1,185 +0,0 @@ - - - 2658 - Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency - true - 191 - - - ncb - ncb@sanger.ac.uk - Nathalie C Smerdon - 191 - - - - - ola - ola@ebi.ac.uk - Aleksandra Kolodziejczyk - 762 - - - - - 2013-06-06 21:47:20 +0100 - 2013-06-06 21:47:32 +0100 - - - Study description - This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes, e.g. Nanog, in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study, we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum/LIF and 2i/LIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network. - - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - - - - Abstract - This study aims to investigate the transcriptomic heterogeneity of mouse embryonic stem cells (mES cells) in different culturing conditions with single-cell mRNA-seq technology. Previous studies have reported heterogeneous and differential allelic expression of specific pluripotency genes, e.g. Nanog, in mES cells in different culturing conditions. The fluctuation of gene expression has been linked to drift of pluripotent state. In this study, we will dissect the transcriptome of mouse ES cells culturing in conventiaonal serum/LIF and 2i/LIF conditions at the single-cell level. The usage of a hybrid mouse ES cell line in this study provides additional insight into differential allelic expression in these two culturing conditions. The data generated in this study will shed light on the regulation of pluripotency network. - - - - - Title - Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency - - - ENA Study Accession Number - ERP003293 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - No - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - open - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - E-ERAD-186 - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - 1.0 - - - HMDMC approval number - - - - Study Type - Transcriptome Analysis - - - What sort of study is this? - transcriptomics - - - Reference Genome - Mus_musculus (NCBIm37) - - - Faculty Sponsor - Sarah Teichmann - - - diff --git a/t/data/samplesheet/st/studies/521.xml b/t/data/samplesheet/st/studies/521.xml deleted file mode 100644 index 50715a37..00000000 --- a/t/data/samplesheet/st/studies/521.xml +++ /dev/null @@ -1,171 +0,0 @@ - - - 521 - Strongyloides ratti transcriptomics - true - 143 - - - dg8 - dg8@sanger.ac.uk - Daria Gordon - 403 - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - - - 2010-04-06 17:05:29 +0100 - 2010-09-17 13:53:35 +0100 - - - EGA Policy Accession Number - - - - Abstract - Transcriptome sequencing of Strongyloides ratti - - - Number of gigabases per sample (minimum 0.15) - - - - Comment regarding prevention of data release and approval - - - - What is the reason for preventing data release? - - - - Policy - - - - Alignments in BAM - true - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - EGA DAC Accession Number - - - - Delay for - - - - Study description - Strongyloides ratti is a common gastro-intestinal parasite of the rat. The adult parasites are female only, about 2mm long and live in the mucosa of the small intestine. These parasites produce eggs that pass out of the host in its faeces. In the environment infective larval stages develop either directly or after a facultative sexual free-living adult generation. Infective larvae infect hosts by skin penetration. - -S. ratti is the laboratory analogue of the parasite of humans, S. stercoralis. S. stercoralis is a wide-spread parasite of humans, occurring principally in the tropics and sub-tropics: some 100-200 million people are infected worldwide. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body. This can be fatal unless anti-Strongyloides therapy is given. Other species of Strongyloides parasitise a wide range of vertebrates. - -As part of the Strongyloides ratti genome project we are profiling the transcriptome of the parasite across its life cycle using RNA-Seq.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - How is the data release to be timed? - standard - - - Study name abbreviation - - - - ENA Study Accession Number - - - - Title - Transcriptome sequencing of Strongyloides ratti - - - SNP study ID - - - - What is the data release strategy for this study? - open - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - No - - - Study Visibility - hold - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - ArrayExpress Accession Number - - - - Reason for delaying release - - - - ENA Project ID - - - - SNP parent study ID - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Comment regarding data release timing and approval - - - - Will you be using WTSI's standard access agreement? - - - - Study Type - Transcriptome Analysis - - - What sort of study is this? - transcriptomics - - - Faculty Sponsor - Matt Berriman - - - Reference Genome - - - - diff --git a/t/data/samplesheet/st/studies/700.xml b/t/data/samplesheet/st/studies/700.xml deleted file mode 100644 index 717cba9c..00000000 --- a/t/data/samplesheet/st/studies/700.xml +++ /dev/null @@ -1,175 +0,0 @@ - - - 700 - Kapa HiFi test - true - 7 - - - mq1 - mq1@sanger.ac.uk - Michael Quail - 7 - - - ems - ems@sanger.ac.uk - Elizabeth Sheridan - 72 - - - - - mq1 - mq1@sanger.ac.uk - Michael Quail - 7 - - - - - 2010-10-07 16:11:00 +0100 - 2010-10-21 11:03:52 +0100 - - - Number of gigabases per sample (minimum 0.15) - - - - Has this been approved? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - ENA Study Accession Number - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - ArrayExpress Accession Number - - - - Title - hifi test - - - ENA Project ID - 0 - - - What is the data release strategy for this study? - not applicable - - - Study Visibility - Hold - - - EGA Policy Accession Number - - - - Study name abbreviation - - - - SNP study ID - - - - What is the reason for preventing data release? - data validity - - - Has the delay period been approved by the data sharing committee for this project? - - - - Do any of the samples in this study contain human DNA? - No - - - Abstract - Purpose of experiment - -- To evaluate kapa hifi qPCR kit -- To evaluate kapa hifi and "robust" enzymes as alternatives to phusion. How do libraries prepared with these enzymes compare in terms of fidelity and coverage? -- To generate data on test genomes that can be used in Pacbio data analysis - - - - Study description - - I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. -- If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage. -- In theory kapa hifi has higher fidelity than phusion. - - - - Alignments in BAM - true - - - Will you be using WTSI's standard access agreement? - - - - Comment regarding prevention of data release and approval - R+D Project - - - EGA DAC Accession Number - - - - Policy - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Reason for delaying release - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - Delay for - - - - How is the data release to be timed? - never - - - Reference Genome - - - - What sort of study is this? - genomic sequencing - - - Faculty Sponsor - Harold Swerdlow - - - Study Type - Whole Genome Sequencing - - - From 452b87d4204ff1bdd51686f9a99d45ca47c1f24a Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 29 Sep 2023 10:20:39 +0100 Subject: [PATCH 04/35] Use correct name instrument name pattern in docs. --- docs/instruments.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/instruments.md b/docs/instruments.md index 64eee8ea..1533bb64 100644 --- a/docs/instruments.md +++ b/docs/instruments.md @@ -18,7 +18,7 @@ perl -le 'use strict; use npg_tracking::Schema; my $s=npg_tracking::Schema->conn NovaSeqX instrument: ``` -perl -le 'use strict; use npg_tracking::Schema; my $s=npg_tracking::Schema->connect(); $s->txn_do(sub{my $m=$s->resultset(q(Instrument))->find_or_create({name=>q[NVX1], instrument_format=>{model=>q(NovaSeqX)}}); $m->update({iscurrent=>1, external_name=>q(Pi1-9)}); $m->add_to_designations({description=>q(Accepted)}); print join",",$m->get_columns; print join",",$_->get_columns foreach $m->designations; print "current instrument status: ".$m->current_instrument_status;});' +perl -le 'use strict; use npg_tracking::Schema; my $s=npg_tracking::Schema->connect(); $s->txn_do(sub{my $m=$s->resultset(q(Instrument))->find_or_create({name=>q[NX1], instrument_format=>{model=>q(NovaSeqX)}}); $m->update({iscurrent=>1, external_name=>q(Pi1-9)}); $m->add_to_designations({description=>q(Accepted)}); print join",",$m->get_columns; print join",",$_->get_columns foreach $m->designations; print "current instrument status: ".$m->current_instrument_status;});' ``` ## Delete Instrument From a82cf95c4ee1cea365888936b27072f63684c0a9 Mon Sep 17 00:00:00 2001 From: mgcam Date: Thu, 5 Oct 2023 15:14:09 +0100 Subject: [PATCH 05/35] Deleted the xml driver for st::api::lims. (#758) * Deleted the xml driver for st::api::lims. * Simplified code for insert size and restored is tests. * Restored previously available tests. Used existing test fixtures, which had to be changed in a few places. --- MANIFEST | 3 - lib/st/api/lims.pm | 50 +- lib/st/api/lims/xml.pm | 990 -------------- t/40-st-lims-insert_size.t | 108 -- t/40-st-lims-samplesheet.t | 2 +- t/40-st-lims.t | 1140 +++++------------ t/45-st-api-lims-traversal.t | 111 -- t/47-samplesheet.t | 2 +- .../000-Sample.yml | 2 +- .../000-Study.yml | 6 +- .../100-IseqFlowcell.yml | 2 +- t/data/samplesheet/4pool4libs_extended.csv | 2 +- t/data/samplesheet/6946_extended.csv | 24 +- 13 files changed, 374 insertions(+), 2068 deletions(-) delete mode 100644 lib/st/api/lims/xml.pm delete mode 100755 t/40-st-lims-insert_size.t delete mode 100644 t/45-st-api-lims-traversal.t diff --git a/MANIFEST b/MANIFEST index 6990c596..f6ae9ff0 100644 --- a/MANIFEST +++ b/MANIFEST @@ -282,7 +282,6 @@ lib/st/api/lims/ml_warehouse/driver.pm lib/st/api/lims/ml_warehouse.pm lib/st/api/lims/ml_warehouse_auto.pm lib/st/api/lims/ml_warehouse_fc_cache.pm -lib/st/api/lims/xml.pm lib/st/api/project.pm lib/st/api/sample.pm lib/st/api/study.pm @@ -408,7 +407,6 @@ t/34-monitor-staging.t t/35-monitor_one_runfolder.t t/40-st-base.t t/40-st-batch.t -t/40-st-lims-insert_size.t t/40-st-lims-mlwarehouse.t t/40-st-lims-ml_warehouse-drivers.t t/40-st-lims-samplesheet.t @@ -416,7 +414,6 @@ t/40-st-lims.t t/40-st-project.t t/40-st-sample.t t/40-st-study.t -t/45-st-api-lims-traversal.t t/47-samplesheet.t t/47-npg_samplesheet_novaseq_xseries.t t/47-npg_samplesheet_auto.t diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 0cf31e44..2790c40e 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -139,9 +139,9 @@ Readonly::Hash my %METHODS_PER_CATEGORY => { 'request' => [qw/ request_id /], }; -Readonly::Array my @METHODS => sort map { @{$_} } values %METHODS_PER_CATEGORY; -Readonly::Array my @DELEGATED_METHODS => sort map { @{$METHODS_PER_CATEGORY{$_}} } - grep {$_ ne 'primary'} keys %METHODS_PER_CATEGORY; +Readonly::Array my @METHODS => sort map { @{$_} } values %METHODS_PER_CATEGORY; +Readonly::Array my @DELEGATED_METHODS => sort map { @{$METHODS_PER_CATEGORY{$_}} } + grep {$_ ne 'primary'} keys %METHODS_PER_CATEGORY; has '_driver_arguments' => ( isa => 'HashRef', @@ -247,7 +247,7 @@ foreach my $object_type (keys %ATTRIBUTE_LIST_METHODS) { =head2 driver_type -Driver type (xml, etc), currently defaults to xml +Driver type, currently defaults to 'samplesheet' =cut has 'driver_type' => ( isa => 'Str', @@ -257,7 +257,7 @@ has 'driver_type' => ( isa => 'Str', ); sub _build_driver_type { my $self = shift; - if($self->has_driver && $self->driver){ + if ($self->has_driver && $self->driver){ my $type = ref $self->driver; my $prefix = __PACKAGE__ . q(::); $type =~ s/\A\Q$prefix\E//smx; @@ -273,7 +273,7 @@ sub _build_driver_type { =head2 driver -Driver object (xml, warehouse, mlwarehouse, samplesheet ...) +Driver object (mlwarehouse, samplesheet) =cut has 'driver' => ( 'isa' => 'Maybe[Object]', @@ -530,7 +530,7 @@ sub _build_tags { =head2 required_insert_size Read-only accessor, not possible to set from the constructor. -Returns a has reference of expected insert sizes. +Returns a hash reference of expected insert sizes. =cut has 'required_insert_size' => (isa => 'HashRef', @@ -542,44 +542,28 @@ sub _build_required_insert_size { my $self = shift; my $is_hash = {}; - my $size_element_defined = 0; - if (defined $self->position && !$self->is_control) { + if (defined $self->position) { my @alims = $self->associated_lims; - if (!@alims) { - @alims = ($self); - } + @alims = @alims ? @alims : ($self); foreach my $lims (@alims) { - $self->_entity_required_insert_size($lims, $is_hash, \$size_element_defined); - } - } - return $is_hash; -} -sub _entity_required_insert_size { - my ($self, $lims, $is_hash, $isize_defined) = @_; - - if (!$is_hash) { - croak q[Isize hash ref should be supplied]; - } - if (!$lims) { - croak q[Lims object should be supplied]; - } - - if (!$lims->is_control) { - my $is = $lims->required_insert_size_range; - if ($is && keys %{$is}) { - ${$isize_defined} = 1; + if ($lims->is_control) { + next; + } + my $is = $lims->required_insert_size_range || {}; foreach my $key (qw/to from/) { my $value = $is->{$key}; if ($value) { - my $lib_key = $lims->library_id || $lims->tag_index || $lims->sample_id; + my $lib_key = $lims->library_id || $lims->sample_id; $is_hash->{$lib_key}->{$key} = $value; } } } } - return; + + return $is_hash; } + =head2 seq_qc_state 1 for passes, 0 for failed, undef if the value is not set. diff --git a/lib/st/api/lims/xml.pm b/lib/st/api/lims/xml.pm deleted file mode 100644 index 7b6db528..00000000 --- a/lib/st/api/lims/xml.pm +++ /dev/null @@ -1,990 +0,0 @@ -package st::api::lims::xml; - -use Carp; -use English qw(-no_match_vars); -use Moose; -use MooseX::StrictConstructor; -use XML::LibXML; -use Readonly; - -use st::api::batch; -use npg_tracking::util::types; - -with qw/ npg_tracking::glossary::run - npg_tracking::glossary::lane - npg_tracking::glossary::tag - /; - -our $VERSION = '0'; - -=head1 NAME - -st::api::lims::xml - -=head1 SYNOPSIS - - $lims = st::api::lims::xml->new(batch_id => 222) #run (batch) level object - $lims = st::api::lims::xml->new(batch_id => 222, position => 3) # lane level object - $lims = st::api::lims::xml->new(batch_id => 222, position => 3, tag_index => 44) # plex level object - -=head1 DESCRIPTION - -Gateway to Sequencescape LIMS. - -=head1 SUBROUTINES/METHODS - -=cut - -Readonly::Scalar our $BAD_SAMPLE_ID => 4; -Readonly::Array our @LIMS_OBJECTS => qw/sample study project/; - -Readonly::Hash our %DELEGATION => { - 'sample' => { - sample_name => 'name', - organism_taxon_id => 'taxon_id', - organism => 'organism', - sample_common_name => 'common_name', - sample_public_name => 'public_name', - sample_accession_number => 'accession_number', - sample_consent_withdrawn => 'consent_withdrawn', - sample_description => 'description', - }, - 'study' => { - study_name => 'name', - email_addresses => 'email_addresses', - email_addresses_of_managers => 'email_addresses_of_managers', - email_addresses_of_followers => 'email_addresses_of_followers', - email_addresses_of_owners => 'email_addresses_of_owners', - study_alignments_in_bam => 'alignments_in_bam', - study_accession_number => 'accession_number', - study_title => 'title', - study_description => 'description', - study_separate_y_chromosome_data => 'separate_y_chromosome_data', - }, - 'project' => { - project_name => 'name', - project_cost_code => 'project_cost_code', - }, -}; - -=head2 id_run - -Run id, optional attribute, redundant, retained for compatibility -with old code and tests. - -=cut -has '+id_run' => (required => 0,); - -=head2 position - -Position, optional attribute. - -=cut -has '+position' => (required => 0,); - -=head2 batch_id - -Batch id. This attribute is kept as optional to retain compatibility -with old code and tests. To retrieve LIMS data, the attribute should -be set by the caller. - -=cut -has 'batch_id' => (isa => 'NpgTrackingPositiveInt', - is => 'ro', - lazy_build => 1, - ); -sub _build_batch_id { - my $self = shift; - croak q[Cannot build batch_id]; -} - -has 'purpose' => (isa => 'Str', is => 'ro', default => 'standard'); - -has '_lane_elements' => (isa => 'ArrayRef', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build__lane_elements { - my $self = shift; - my $doc = st::api::batch->new({id => $self->batch_id,})->read(); - if(!$doc) { - croak q[Failed to load XML for batch] . $self->batch_id; - } - my $lanes = $doc->getElementsByTagName(q[lanes])->[0]; - if (!$lanes) { - croak q[Lanes element is not defined in batch ] . $self->batch_id; - } - my @nodes = $lanes->getElementsByTagName(q[lane]); - return \@nodes; -} - -=head2 _associated_lims - -Private accessor, not possible to set from the constructor. -Use associated_lims method. - -=cut -has '_associated_lims' => (isa => 'Maybe[ArrayRef]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - clearer => 'free_children', - ); -sub _build__associated_lims { - my $self = shift; - - my $lims = []; - - if (!defined $self->position) { - foreach my $lane_el (@{$self->_lane_elements}) { - my $position = $lane_el->getAttribute(q[position]); - if (!$position) { - croak q[Position is not defined for one of the lanes in batch ] . $self->batch_id; - } - - my $h = { - batch_id => $self->batch_id, - position => $position, - _lane_xml_element => $lane_el, - }; - if (defined $self->id_run) { $h->{id_run} = $self->id_run; } - push @{$lims}, st::api::lims::xml->new($h); - } - } else { - if ($self->is_pool && !$self->tag_index) { #now use XPath to find tag indexes for lane...: - foreach my $tag_index (sort {$a <=> $b} map{$_->textContent}$self->_lane_xml_element->findnodes(q(*/sample/tag/index))) { - my $h = { - batch_id => $self->batch_id, - position => $self->position, - tag_index => $tag_index, - _lane_xml_element => $self->_lane_xml_element, - }; - if (defined $self->id_run) { $h->{id_run} = $self->id_run; } - push @{$lims}, st::api::lims::xml->new($h); - } - } - } - return $lims; -} - -=head2 _lane_xml_element - -Private accessor. XML::LibXML::Element fragment of batch xml representing a lane. -Build only if the position accessor is set. - -=cut -has '_lane_xml_element' => (isa => 'Maybe[XML::LibXML::Element]', - is => 'ro', - lazy_build => 1, - ); -sub _build__lane_xml_element { - my $self = shift; - - if (!defined $self->position) { return; } - - foreach my $lane_el (@{$self->_lane_elements}) { - if($self->position == $lane_el->getAttribute(q[position])) { - return $lane_el; - } - } - croak q[Lane ] . $self->position . q[ is not defined in ] . $self->to_string; -} - -=head2 _entity_xml_element - -Private accessor. XML::LibXML::Element fragment of batch xml representing a low-lelel entity, -such as library, whether a whole lane, a plex, a control, or spiked phix. -Build only if the position accessor is set. - -=cut -has '_entity_xml_element' => (isa => 'Maybe[XML::LibXML::Element]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build__entity_xml_element { - my $self = shift; - - if (!$self->_lane_xml_element) { return; } - - my $element; - my $is_control = $self->_lane_xml_element->getChildrenByTagName(q[control]) ? 1 : 0; - my $has_pool_element = $self->_lane_xml_element->getChildrenByTagName(q[pool]) ? 1 :0; - my $is_pool = ! defined $self->tag_index && $has_pool_element ? 1 :0; - - my $plexes = - $has_pool_element ? $self->_lane_xml_element->getElementsByTagName(q[sample]) : undef; - if ($self->tag_index) { - if (!$plexes || !@{$plexes}) { - croak 'No plexes defined for lane ' . $self->position . q[ in batch ] . $self->batch_id; - } - if ($plexes) { - foreach my $plex (@{$plexes}) { - my $iel = $plex->getElementsByTagName(q[index]); - if ($iel) { - my $index = $iel->[0]->textContent(); - if($self->tag_index == $index) { - $element = $plex; - $is_control ||= $plex->parentNode->nodeName() eq q{hyb_buffer} ? 1 : 0; - last; - } - } - } - } - - if (!$element) { - my $buffer = $self->_lane_xml_element->getChildrenByTagName(q[hyb_buffer]); - if ($buffer) { - $buffer = $buffer->[0]; - my $el = $buffer->getElementsByTagName(q[index]); - if ($el) { - if ($el->[0]->textContent() == $self->tag_index) { - $is_control = 1; - $element = $buffer; - } - } - } - } - - if (!$element) { - croak q[No tag with index ] . $self->tag_index . q[ in lane ] . $self->position . q[ batch ] . $self->batch_id; - } - } else { - $is_pool = $plexes ? 1 : 0; - my $control = $self->_lane_xml_element->getChildrenByTagName(q[control]); - if ($control && @{$control}) { - $element = $control->[0]; - $is_control = 1; - } else { - my $ename = $is_pool ? q[pool] : q[library]; - $element = $self->_lane_xml_element->getChildrenByTagName($ename)->[0]; - } - } - - $self->_set_is_control($is_control); - $self->_set_is_pool($is_pool); - - return $element; -} - -=head2 _subentity_xml_element - -Private accessor. XML::LibXML::Element fragment of batch xml representing a sample element -(where available) within _entity_xml_element. -Build only if the position accessor is set. - -=cut -has '_subentity_xml_element' => (isa => 'Maybe[XML::LibXML::Element]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build__subentity_xml_element { - my $self = shift; - - if (!$self->_entity_xml_element || $self->is_pool || defined $self->tag_index) { return; } - my $subentity = $self->_entity_xml_element->getChildrenByTagName(q[sample])->[0] || undef; - return $subentity; -} - -=head2 default_tag_sequence - -Read-only string accessor, not possible to set from the constructor. -Undefined on a lane level and for zero tag_index. - -=cut -has 'default_tag_sequence' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_default_tag_sequence { - my $self = shift; - return $self->_get_tag_sequence('tag_id'); -} - -=head2 default_tag2_sequence - -Read-only string accessor, not possible to set from the constructor. -Undefined on a lane level and for zero tag_index. - -=cut -has 'default_tagtwo_sequence' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_default_tagtwo_sequence { - my $self = shift; - return $self->_get_tag_sequence('tag2_id'); -} - -sub _get_tag_sequence { - my ($self, $tag_sequence_name) = @_; - - if (!$tag_sequence_name) { - croak 'Need tag sequence element name'; - } - - my $seq; - if ($self->tag_index) { - if ($self->_entity_xml_element) { - - my @tag_elts = grep { $_->hasAttribute($tag_sequence_name) } $self->_entity_xml_element->getElementsByTagName(q[tag]); - if (scalar @tag_elts > 1) { - croak "Multiple tag entries for $tag_sequence_name"; - } - if (@tag_elts) { - my $sel = $tag_elts[0]->getElementsByTagName(q[expected_sequence]); - if ($sel) { - $seq = $sel->[0]->textContent(); - } - } - } - } - - return $seq; -} - -=head2 spiked_phix_tag_index - -Read-only integer accessor, not possible to set from the constructor. -Defined for a lane and all tags, including tag zero - -=cut -has 'spiked_phix_tag_index' => (isa => 'Maybe[NpgTrackingTagIndex]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_spiked_phix_tag_index { - my $self = shift; - - if ($self->_lane_xml_element) { - my $buffer = $self->_lane_xml_element->getElementsByTagName(q[hyb_buffer]); - if ($buffer) { - my $el = $buffer->[0]->getElementsByTagName(q[index]); - if ($el) { - return $el->[0]->textContent(); - } else { - croak 'should be spiked phix, but tag index is not defined'; - } - } - } - return; -} - -=head2 is_control - -Read-only boolean accessor, not possible to set from the constructor. -True for a control lane and for the spiked phix plex, otherwise false. - -=cut -has 'is_control' => (isa => 'Bool', - is => 'ro', - init_arg => undef, - lazy_build => 1, - writer => '_set_is_control', - ); -sub _build_is_control { - my $self = shift; - return $self->_entity_xml_element ? $self->is_control : 0; -} - -=head2 is_pool - -Read-only boolean accessor, not possible to set from the constructor. -True for a pooled lane on a lane level, otherwise false. - -=cut -has 'is_pool' => (isa => 'Bool', - is => 'ro', - init_arg => undef, - lazy_build => 1, - writer => '_set_is_pool', - ); -sub _build_is_pool { - my $self = shift; - return $self->_entity_xml_element ? $self->is_pool : 0; -} - -has 'bait_name' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); - -=head2 bait_name - -Read-only accessor, not possible to set from the constructor. -Returns the name of the bait if given. For a pooled lane, for a control of if no bait given, -returns undefined value. - -=cut -sub _build_bait_name { - my $self = shift; - - my $bait_name; - if (!$self->is_pool && !$self->is_control && $self->_entity_xml_element) { - my $be = $self->_entity_xml_element->getElementsByTagName(q[bait]); - if ($be) { - $be = $be->[0]->getElementsByTagName('name'); - if ($be) { - $bait_name = $be->[0]->textContent(); - } - } - } - $bait_name ||= undef; - return $bait_name; -} - -=head2 lane_id - -For a lane level object returns the unique id (asset id) of the lane, -for other levels undefined. Read-only accessor, not possible to set from the constructor. - -=cut -has 'lane_id' => ( isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_lane_id { - my $self = shift; - - my $id; - if ( defined $self->position() && !defined $self->tag_index() ) { - $id = $self->_lane_xml_element()->getAttribute('id'); - } - $id ||= undef; - return $id; -} - -=head2 lane_priority - -For a lane level object returns this lane priority, -for other levels undefined. Read-only accessor, not possible to set from the constructor. - -=cut -has 'lane_priority' => ( isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_lane_priority { - my $self = shift; - - my $id = undef; - if ( defined $self->position() && !defined $self->tag_index() ) { - $id = $self->_lane_xml_element()->getAttribute('priority'); - } - return $id; -} - -=head2 library_id - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'library_id' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_library_id { - my $self = shift; - - if(!$self->_xml_element_exists(q[entity])) { return; } - - my $id = $self->_entity_xml_element->getAttribute('id'); - if (!$id) { - $id = $self->_entity_xml_element->getAttribute('library_id'); - } - $id ||= undef; - return $id; -} - -=head2 library_name - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'library_name' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_library_name { - my $self = shift; - - if(!$self->_xml_element_exists(q[entity])) { return; } - - my $name; - my $element = $self->_entity_xml_element; - if ($self->is_pool) { - $name = $element->getAttribute(q[name]); - } else { - if (!$self->tag_index) { - $element = $self->_subentity_xml_element; - } - if ($element) { - $name = $element->getAttribute(q[library_name]); - } - } - $name ||= undef; - return $name; -} - -=head2 default_library_type - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'default_library_type' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_default_library_type { - my $self = shift; - - if(!$self->_xml_element_exists(q[entity]) || $self->is_pool) { return; } - - my $element = $self->tag_index ? $self->_entity_xml_element : $self->_subentity_xml_element; - my $type; - if ($element) { - $type = $element->getAttribute(q[library_type]); - } - $type ||= undef; - return $type; -} - -=head2 sample_id - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'sample_id' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_sample_id { - my $self = shift; - - if(!$self->_xml_element_exists(q[entity])) { return; } - - my $sample_id = $self->_entity_xml_element->getAttribute(q[sample_id]); - if (!$sample_id && $self->_subentity_xml_element) { - $sample_id = $self->_subentity_xml_element->getAttribute(q[sample_id]); - } - if ($sample_id && $sample_id == $BAD_SAMPLE_ID) { - warn qq[Resetting magic sample id $BAD_SAMPLE_ID to undef\n]; - $sample_id = undef; - } - $sample_id ||= undef; - return $sample_id; -} - -=head2 study_id - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'study_id' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_study_id { - my $self = shift; - if(!$self->_xml_element_exists(q[entity])) { return; } - my $study_id = $self->_entity_xml_element->getAttribute(q[study_id]); - if (!$study_id && $self->_subentity_xml_element) { - $study_id = $self->_subentity_xml_element->getAttribute(q[study_id]); - } - $study_id ||= undef; - return $study_id; -} - -=head2 project_id - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'project_id' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_project_id { - my $self = shift; - - if(!$self->_xml_element_exists(q[entity])) { return; } - my $project_id = $self->_entity_xml_element->getAttribute(q[project_id]); - if (!$project_id && $self->_subentity_xml_element) { - $project_id = $self->_subentity_xml_element->getAttribute(q[project_id]); - } - $project_id ||= undef; - return $project_id; -} - -=head2 request_id - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'request_id' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_request_id { - my $self = shift; - - if(!$self->_xml_element_exists(q[entity])) { return; } - my $request_id = $self->_entity_xml_element->getAttribute(q[request_id]) || undef; - return $request_id; -} - -=head2 qc_state - -Read-only accessor, not possible to set from the constructor. - -=cut -has 'qc_state' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_qc_state { - my $self = shift; - if ($self->_xml_element_exists(q[entity])) { - return $self->_entity_xml_element->getAttribute(q[qc_state]); - } - return; -} - -sub _build__library_object { - my $self = shift; - return $self->_lims_object(q[library]); -} -sub _build__sample_object { - my $self = shift; - return $self->_lims_object(q[sample]); -} -sub _build__study_object { - my $self = shift; - return $self->_lims_object(q[study]); -} -sub _build__project_object { - my $self = shift; - return $self->_lims_object(q[project]); -} -sub _build__request_object { - my $self = shift; - return $self->_lims_object(q[request]); -} - -foreach my $object_type ( @LIMS_OBJECTS ) { - - my $st_type = $object_type eq q[library] ? q[asset] : $object_type; - my $isa = q{Maybe[st::api::} . $st_type . q{]}; - my $attr_name = join q[_], q[], $object_type, q[object]; - has $attr_name => ( is => 'ro', isa => $isa, init_arg => undef, lazy_build => 1, handles => $DELEGATION{$object_type}); - - if (scalar keys %{$DELEGATION{$object_type}} == 0) { next; } - for my $func (keys %{$DELEGATION{$object_type}}) { - around $func => sub { - my ($orig, $self) = @_; - return $self->$attr_name ? $self->$orig() : undef; - }; - } -} - -=head2 required_insert_size_range - -Read-only accessor, not possible to set from the constructor. -Returns a has reference of expected insert sizes. - -=cut -has 'required_insert_size_range' => (isa => 'HashRef', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_required_insert_size_range { - my $self = shift; - - my $is_hash = {}; - if (!$self->is_control) { - my $is_element = $self->_entity_xml_element->getElementsByTagName(q[insert_size]); - if ($is_element) { - $is_element = $is_element->[0]; - } - if ($is_element) { - foreach my $key (qw/to from/) { - my $value = $is_element->getAttribute($key); - if ($value) { - $is_hash->{$key} = $value; - } - } - } - } - return $is_hash; -} - -=head2 sample_reference_genome - -Read-only accessor, not possible to set from the constructor. -Returns sample reference genome - -=cut -has 'sample_reference_genome' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_sample_reference_genome { - my $self = shift; - my $rg; - if ($self->_sample_object) { - $rg = $self->_sample_object->reference_genome; - } - return $rg; -} - -=head2 study_reference_genome - -Read-only accessor, not possible to set from the constructor. -Returns study reference genome - -=cut -has 'study_reference_genome' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_study_reference_genome { - my $self = shift; - my $rg; - if ($self->_study_object) { - $rg = $self->_study_object->reference_genome; - } - return $rg; -} - -=head2 study_contains_nonconsented_human - -Read-only accessor, not possible to set from the constructor. -For a library, control on non-zero plex returns the value of the -contains_nonconsented_human on the relevant study object. For a pool -or a zero plex returns 1 if any of the studies in the pool -contein unconcented human. - -On a batch level or if no associated study found, returns 0. - -=cut -has 'study_contains_nonconsented_human' => (isa => 'Bool', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_study_contains_nonconsented_human { - my $self = shift; - - my $cuh = 0; - if ($self->position && $self->_study_object) { - $cuh = $self->_study_object->contains_nonconsented_human; - } - if (!$cuh) { $cuh = 0; } - return $cuh; -} - -=head2 study_contains_nonconsented_xahuman - -Read-only accessor, not possible to set from the constructor. -For a library, control on non-zero plex returns the value of the -contains_nonconsented_xahuman on the relevant study object. For a pool -or a zero plex returns 1 if any of the studies in the pool -contain unconcented X and autosomal human. - -On a batch level or if no associated study found, returns 0. - -=cut -has 'study_contains_nonconsented_xahuman' => (isa => 'Bool', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); -sub _build_study_contains_nonconsented_xahuman { - my $self = shift; - - my $cuh = 0; - if ($self->position && $self->_study_object) { - $cuh = $self->_study_object->contains_nonconsented_xahuman; - } - if (!$cuh) { $cuh = 0; } - return $cuh; -} - -=head2 children - -Method returning a list of st::api::lims::xml objects that are associated with this object -and belong to the next (one lower) level. An empty list for a non-pool lane and for a plex. -For a pooled lane contains plex-level objects. On a batch level, when the position -accessor is not set, returns lane level objects. - -=cut -sub children { - my $self = shift; - return @{$self->_associated_lims}; -} - - -=head2 method_list - -Method returning a sorted list of useful accessors and methods. - -=cut -sub method_list { - my $self = shift; - my @attrs = (); - foreach my $name (__PACKAGE__->meta->get_attribute_list) { - if ($name =~ /^\_/smx) { - next; - } - push @attrs, $name; - } - - foreach my $object_type ( @LIMS_OBJECTS ) { - my @functions = keys %{$DELEGATION{$object_type}}; - if (@functions) { - push @attrs, @functions; - } - } - - @attrs = sort @attrs; - return @attrs; -} - -sub _lims_object { - my ($self, $object_type) = @_; - - my $class = q[st::api::] . $object_type; - my $method = join q[_], $object_type, q[id]; - my $id = $self->$method; - - if ($id) { - ## no critic (ProhibitStringyEval RequireCheckingReturnValueOfEval) - eval "require $class"; - ## use critic - return $class->new({id => $id,}); - } - return; -} - -sub _xml_element_exists { - my ($self, $el_type) = @_; - - if ($el_type ne q[lane] && $el_type ne q[entity]) { - croak qq[Unknown xml element type $el_type in _validate_xml_element]; - } - - my $attr = join q[_], q[], $el_type, q[xml], q[element]; - if(!$self->$attr) { - if ($self->position) { - croak qq[$attr attribute not defined in ] . $self->to_string; - } - return 0; - } - return 1; -} - -=head2 to_string - -Human friendly description of the object - -=cut -sub to_string { - my $self = shift; - - my $s = __PACKAGE__ . q[ object for batch ] . $self->batch_id; - if (defined $self->position) { - $s .= q[ position ] . $self->position; - } - if (defined $self->tag_index) { - $s .= q[ tag_index ] . $self->tag_index; - } - return $s; -} - -__PACKAGE__->meta->make_immutable; -no Moose; - -1; -__END__ - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item Moose - -=item MooseX::StrictConstructor - -=item Carp - -=item English - -=item Readonly - -=item XML::LibXML - -=item npg::api::run - -=item st::api::batch - -=item npg_tracking::util::types - -=item npg_tracking::glossary::run - -=item npg_tracking::glossary::lane - -=item npg_tracking::glossary::tag - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Marina Gourtovaia Emg8@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2013,2014,2015,2016,2021 Genome Research Ltd. - -This file is part of NPG. - -NPG is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut diff --git a/t/40-st-lims-insert_size.t b/t/40-st-lims-insert_size.t deleted file mode 100755 index 2fde2793..00000000 --- a/t/40-st-lims-insert_size.t +++ /dev/null @@ -1,108 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 40; -use Test::Exception; - -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = q[t/data/test40_lims_edited]; - -use_ok('st::api::lims'); - -{ - my $lims = st::api::lims->new( - batch_id => 4775, position => 1, driver_type => 'xml'); - my $lid = $lims->library_id; - - my $is_available = 0; - my $is = {}; - $lims->_entity_required_insert_size($lims, $is, \$is_available); - is (keys %{$is}, 1, 'one entry in the insert size hash'); - is ($is->{$lid}->{q[from]}, 300, 'required FROM insert size'); - is ($is->{$lid}->{q[to]}, 400, 'required TO insert size'); - is ($is_available, 1, 'is reported as available'); - - $is_available = 1; - $lims->_entity_required_insert_size($lims, $is, \$is_available); - is ($is_available, 1, 'is reported as available'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 2, driver_type => 'xml'); - $is = {}; - $is_available = 0; - $lims->_entity_required_insert_size($lims, $is, \$is_available); - is (keys %{$is}, 0, 'the insert size hash is empty'); - is ($is_available, 0, 'is reported as not available'); - - $is_available = 1; - $lims->_entity_required_insert_size($lims, $is, \$is_available); - is ($is_available, 1, 'is reported as available'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 3, driver_type => 'xml'); - $is = {}; - $is_available = 0; - $lims->_entity_required_insert_size($lims, $is, \$is_available); - is (keys %{$is}, 0, 'the insert size hash is empty'); - is ($is_available, 0, 'is reported as not available'); -} - -{ - my $lims = st::api::lims->new( - batch_id => 4775, position => 1, driver_type => 'xml'); - my $lid = $lims->library_id; - my $insert_size; - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the first lane lives'; - is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); - is ($insert_size->{$lid}->{q[from]}, 300, 'required FROM insert size'); - is ($insert_size->{$lid}->{q[to]}, 400, 'required TO insert size'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 3, driver_type => 'xml'); - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the third lane where empty is hash is returned lives'; - is (keys %{$insert_size}, 0, 'no entries in the insert size hash'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 4, driver_type => 'xml'); - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the control lane lives'; - is (keys %{$insert_size}, 0, 'no entries in the insert size hash'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 8, driver_type => 'xml'); - ok ($lims ->is_pool, 'lane is a pool'); - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the pool where empty is hash is returned lives'; - is (keys %{$insert_size}, 0, 'no entries in the insert size hash'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 7, driver_type => 'xml'); - ok ($lims ->is_pool, 'lane is a pool'); - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the pool lives'; - is (keys %{$insert_size}, 2, 'two entries in the insert size hash'); - is ($insert_size->{2798524}->{q[from]}, 40, 'required FROM insert size'); - is ($insert_size->{2798524}->{q[to]}, 50, 'required TO insert size'); - ok (!exists $insert_size->{2798525}->{q[from]}, 'no required FROM insert size'); - is ($insert_size->{2798525}->{q[to]}, 500, 'required TO insert size'); - - $lims = st::api::lims->new( - batch_id => 4775, position => 7, tag_index => 2, driver_type => 'xml'); - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the plex lives'; - is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); - is ($insert_size->{2798524}->{q[from]}, 40, 'required FROM insert size'); - is ($insert_size->{2798524}->{q[to]}, 50, 'required TO insert size'); -} - -{ - my $lims = st::api::lims->new( - driver_type => 'xml', batch_id => 14706, position => 1, tag_index => 2); - my $insert_size; - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the plex without lib id lives'; - is ($insert_size->{2}->{q[from]}, 200, 'required FROM insert size'); - is ($insert_size->{2}->{q[to]}, 400, 'required TO insert size'); - - $lims = st::api::lims->new( - driver_type => 'xml', batch_id => 14706, position => 2); - lives_ok {$insert_size = $lims->required_insert_size} 'insert size for the pool with plexes without lib ids lives'; - is (join(q[ ], sort keys %{$insert_size}), '1 2 3 4 5', 'tag index entries in the insert size hash'); - is ($insert_size->{5}->{q[from]}, 200, 'required FROM insert size'); - is ($insert_size->{4}->{q[to]}, 400, 'required TO insert size'); -} - -1; diff --git a/t/40-st-lims-samplesheet.t b/t/40-st-lims-samplesheet.t index c3a10f1e..78c785ed 100644 --- a/t/40-st-lims-samplesheet.t +++ b/t/40-st-lims-samplesheet.t @@ -337,7 +337,7 @@ subtest 'Multiple NovaSeq runs - top-up merge support' => sub { } }; -subtest 'multiple lanes, comparison of xml and samplesheet drivers' => sub { +subtest 'multiple lanes' => sub { plan tests => 5; my $path = 't/data/samplesheet/4pool4libs_extended.csv'; diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 8a9b0193..9bba0b2c 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -1,29 +1,17 @@ use strict; use warnings; -use Test::More tests => 30; +use Test::More tests => 19; use Test::Exception; use Test::Warn; use File::Temp qw/ tempdir /; +use Moose::Meta::Class; my $num_delegated_methods = 48; -local $ENV{'http_proxy'} = 'http://wibble.com'; - use_ok('st::api::lims'); -my %dr = (driver_type =>'xml',); - -subtest 'Class methods' => sub { - plan tests => 10; - - is(st::api::lims->cached_samplesheet_var_name, 'NPG_CACHED_SAMPLESHEET_FILE', - 'correct name of the cached samplesheet env var'); - - is(scalar st::api::lims->driver_method_list(), $num_delegated_methods, 'driver method list length'); - is(scalar st::api::lims::driver_method_list_short(), $num_delegated_methods, 'short driver method list length'); - is(scalar st::api::lims->driver_method_list_short(), $num_delegated_methods, 'short driver method list length'); - is(scalar st::api::lims::driver_method_list_short(qw/sample_name/), $num_delegated_methods-1, 'one method removed from the list'); - is(scalar st::api::lims->driver_method_list_short(qw/sample_name study_name/), $num_delegated_methods-2, 'two methods removed from the list'); +subtest 'Test trim' => sub { + plan tests => 4; my $value = 'some other'; is(st::api::lims->_trim_value($value), $value, 'nothing trimmed'); @@ -32,77 +20,95 @@ subtest 'Class methods' => sub { is(st::api::lims->_trim_value(" "), undef, 'white space string trimmed to undef'); }; -subtest 'Setting return value for primary attributes' => sub { - plan tests => 51; +subtest 'Driver type, methods and driver build' => sub { + plan tests => 27; - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; + my $ss_path = 't/data/samplesheet/miseq_default.csv'; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $ss_path; + my $l; + lives_ok {$l = st::api::lims->new(id_run => 10262,)} + 'no error creating an object with samplesheet file defined in env var'; + is ($l->driver_type, 'samplesheet', 'driver type is built as samplesheet'); + is ($l->path, $ss_path, 'correct path is built'); + is (ref $l->driver, 'st::api::lims::samplesheet', 'correct driver object type'); + is ($l->driver->path, $ss_path, 'correct path assigned to the driver object'); - my @other = qw/path id_flowcell_lims flowcell_barcode/; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet'; + ok (-d $ENV{NPG_CACHED_SAMPLESHEET_FILE}); + lives_ok {$l = st::api::lims->new(id_run => 10262,)} + 'no error creating an object with samplesheet file defined in env var'; + is ($l->driver_type, 'samplesheet', 'driver type is samplesheet'); + throws_ok { $l->path } + qr/Attribute \(path\) does not pass the type constraint/, + 'samplesheet cannot be a directory'; - my $lims = st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 2); - my $lane_lims = $lims; - for my $attr (@other) { - is ($lims->$attr, undef, "$attr is undefined"); - } - is ($lims->id_run, 6551, 'id run is set correctly'); - is ($lims->batch_id, 12141, 'batch id is set correctly'); - is ($lims->position, 2, 'position is set correctly'); - is ($lims->tag_index, undef, 'tag_index is undefined'); - ok ($lims->is_pool, 'lane is a pool'); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/non-existing'; + ok (not -e $ENV{NPG_CACHED_SAMPLESHEET_FILE}); + lives_ok {$l = st::api::lims->new(id_run => 10262,)} + 'no error creating an object with samplesheet file defined in env var'; + is ($l->driver_type, 'samplesheet', 'driver type is samplesheet'); + throws_ok {$l->children} + qr/Attribute \(path\) does not pass the type constraint/, + 'samplesheet file should exist'; - my @children = $lims->children(); - $lims = shift @children; - for my $attr (@other) { - is ($lims->$attr, undef, "$attr is undefined"); - } - is ($lims->id_run, 6551, 'id run is set correctly'); - is ($lims->batch_id, 12141, 'batch id is set correctly'); - is ($lims->position, 2, 'position is set correctly'); - is ($lims->tag_index, 1, 'tag_index is set to 1'); - - $lims = st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 2, tag_index => 0); - for my $attr (@other) { - is ($lims->$attr, undef, "$attr is undefined"); - } - is ($lims->id_run, 6551, 'id run is set correctly'); - is ($lims->batch_id, 12141, 'batch id is set correctly'); - is ($lims->position, 2, 'position is set correctly'); - is ($lims->tag_index, 0, 'tag_index is set to zero'); - ok ($lims->is_pool, 'tag zero is a pool'); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/non-existing'; + lives_ok {$l = st::api::lims->new(id_run => 10262, path => $ss_path)} + 'no error creating an object with samplesheet file defined in env var and path given'; + is ($l->driver_type, 'samplesheet', 'driver type is samplesheet'); + lives_ok {$l->children} 'given path takes precedence'; - $lims = st::api::lims->new(driver => $lane_lims->driver(), - id_run => 6551, batch_id => 12141, position => 2, tag_index => 0); - is ($lims->id_run, 6551, 'id run is set correctly'); - is ($lims->batch_id, 12141, 'batch id is set correctly'); - is ($lims->position, 2, 'position is set correctly'); - is ($lims->tag_index, 0, 'tag_index is set to zero'); - ok ($lims->is_pool, 'tag zero is a pool'); + throws_ok { st::api::lims->new( + id_run => 6551, driver_type => 'some') } + qr/Can\'t locate st\/api\/lims\/some\.pm in \@INC/, + 'unknown driver type specified - error'; - $lims = st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 2, tag_index => 2); - is ($lims->tag_index, 2, 'tag_index is set correctly'); + is (st::api::lims->cached_samplesheet_var_name, 'NPG_CACHED_SAMPLESHEET_FILE', + 'get name of the cached samplesheet env var via a class method'); - my $path = 't/data/samplesheet/miseq_default.csv'; - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $path; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/miseq_default.csv'; + $l = st::api::lims->new(id_run => 6551); + is($l->driver_type, 'samplesheet'); + isa_ok ($l->driver(), 'st::api::lims::samplesheet'); - $lims = st::api::lims->new(id_run => 6551, position => 1, tag_index => 0); - is ($lims->driver_type, 'samplesheet', 'samplesheet driver'); + use_ok('st::api::lims::samplesheet'); + $l = st::api::lims->new(id_run => 6551, + driver => st::api::lims::samplesheet->new( + id_run => 6551, + path => $ENV{NPG_CACHED_SAMPLESHEET_FILE})); + is($l->driver_type, 'samplesheet', 'driver type from the driver object'); - push @other, 'batch_id'; - shift @other; + is(scalar st::api::lims->driver_method_list(), $num_delegated_methods, + 'driver method list length'); + is(scalar st::api::lims::driver_method_list_short(), $num_delegated_methods, + 'short driver method list length'); + is(scalar st::api::lims->driver_method_list_short(), $num_delegated_methods, + 'short driver method list length'); + is(scalar st::api::lims::driver_method_list_short(qw/sample_name/), + $num_delegated_methods-1, 'one method removed from the list'); + is(scalar st::api::lims->driver_method_list_short(qw/sample_name study_name/), + $num_delegated_methods-2, 'two methods removed from the list'); +}; + +subtest 'Setting return value for primary attributes' => sub { + plan tests => 23; + + my @other = qw/batch_id id_flowcell_lims flowcell_barcode/; + my $ss_path = 't/data/samplesheet/miseq_default.csv'; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $ss_path; + + my $lims = st::api::lims->new(id_run => 6551, position => 1, tag_index => 0); + is ($lims->driver_type, 'samplesheet', 'samplesheet driver'); for my $attr (@other) { is ($lims->$attr, undef, "$attr is undefined"); } is ($lims->id_run, 6551, 'id run is set correctly'); - is ($lims->path, $path, 'path is set correctly'); + is ($lims->path, $ss_path, 'path is set correctly'); is ($lims->position, 1, 'position is set correctly'); is ($lims->tag_index, 0, 'tag_index is set to zero'); ok ($lims->is_pool, 'tag zero is a pool'); - $lane_lims = st::api::lims->new(id_run => 6551, position => 1); + my $lane_lims = st::api::lims->new(id_run => 6551, position => 1); $lims = st::api::lims->new(driver => $lane_lims->driver(), id_run => 6551, position => 1, @@ -112,6 +118,10 @@ subtest 'Setting return value for primary attributes' => sub { is ($lims->tag_index, 0, 'tag_index is set to zero'); ok ($lims->is_pool, 'tag zero is a pool'); ok (!$lims->is_composition, 'tag zero is not a composition'); + is($lims->to_string, + 'st::api::lims object, driver - samplesheet, id_run 6551, ' . + 'path t/data/samplesheet/miseq_default.csv, position 1, tag_index 0', + 'object as string'); $lims = st::api::lims->new(rpt_list => '6551:1'); my @a = @other; @@ -123,631 +133,6 @@ subtest 'Setting return value for primary attributes' => sub { } }; -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; - -my @libs_6551_1 = ('PhiX06Apr11','SS109114 2798524','SS109305 2798523','SS117077 2798526','SS117886 2798525','SS127358 2798527','SS127858 2798529','SS128220 2798530','SS128716 2798531','SS129050 2798528','SS129764 2798532','SS130327 2798533','SS131636 2798534'); -my @samples_6551_1 = qw/phiX_for_spiked_buffers SS109114 SS109305 SS117077 SS117886 SS127358 SS127858 SS128220 SS128716 SS129050 SS129764 SS130327 SS131636/; -my @accessions_6551_1 = qw/ERS024591 ERS024592 ERS024593 ERS024594 ERS024595 ERS024596 ERS024597 ERS024598 ERS024599 ERS024600 ERS024601 ERS024602/; -my @studies_6551_1 = ('Illumina Controls','Discovery of sequence diversity in Shigella sp.'); - -subtest 'Driver type and driver build' => sub { - plan tests => 11; - - throws_ok { st::api::lims->new( - id_run => 6551, batch_id => 12141, driver_type => 'some') } - qr/Can\'t locate st\/api\/lims\/some\.pm in \@INC/, - 'unknown driver type specified - error'; - - isa_ok (st::api::lims->new( - id_run => 6551, batch_id => 12141, driver_type => 'xml')->driver(), - 'st::api::lims::xml'); - - is (st::api::lims->cached_samplesheet_var_name, 'NPG_CACHED_SAMPLESHEET_FILE', - 'get name of the cached samplesheet env var via a class method'); - - my $l = st::api::lims->new(id_run => 6551); - is($l->driver_type, 'samplesheet'); - is($l->cached_samplesheet_var_name, 'NPG_CACHED_SAMPLESHEET_FILE', - 'get name of the cached samplesheet env var via an instance method'); - lives_ok { $l->driver() } 'can instantiate samplesheet driver'; - throws_ok { $l->num_children() } - qr/Attribute \(path\) does not pass the type constraint/, - 'no samplesheet file - error invoking a method'; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/miseq_default.csv'; - $l = st::api::lims->new(id_run => 6551); - is($l->driver_type, 'samplesheet'); - isa_ok ($l->driver(), 'st::api::lims::samplesheet'); - - use_ok('st::api::lims::samplesheet'); - $l = st::api::lims->new(id_run => 6551, - driver => st::api::lims::samplesheet->new( - id_run => 6551, - path => $ENV{NPG_CACHED_SAMPLESHEET_FILE})); - is($l->driver_type, 'samplesheet', 'driver type from the driver object'); -}; - -subtest 'Run-level object' => sub { - plan tests => 18; - - my $lims = st::api::lims->new(%dr, id_run => 6551, batch_id => 12141); - is(scalar $lims->driver_method_list_short(), $num_delegated_methods, 'short driver method list lenght from an object'); - is(scalar $lims->driver_method_list_short(qw/sample_name other_name/), $num_delegated_methods-1, 'one method removed from the list'); - is($lims->lane_id(), undef, q{lane_id undef for id_run 6551, not a lane} ); - is($lims->batch_id, 12141, 'batch id is 12141'); - is($lims->is_control, 0, 'not control'); - is($lims->is_pool, 0, 'not pool'); - is($lims->library_id, undef, 'no lib id'); - is($lims->seq_qc_state, undef, 'no seq qc state'); - is($lims->tag_sequence, undef, 'tag_sequence undefined'); - is($lims->tags, undef, 'tags undefined'); - is($lims->spiked_phix_tag_index, undef, 'spiked phix tag index undefined'); - is(scalar $lims->descendants, 185, '185 descendant lims'); - is(scalar $lims->children, 8, '8 child lims'); - is($lims->to_string, 'st::api::lims object, driver - xml, batch_id 12141, id_run 6551', 'object as string'); - is(scalar($lims->library_names), 0, 'batch-level library_names list empty'); - is(scalar($lims->sample_names), 0, 'batch-level sample_names list empty'); - is(scalar($lims->sample_accession_numbers), 0, 'batch-level sample_accession_numbers list empty'); - is(scalar($lims->study_names), 0, 'batch-level study_names list empty'); -}; - -subtest 'Lane-level object' => sub { - plan tests => 103; - - my @lims_list = (); - push @lims_list, st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 1); - my @comps = (); - foreach my $tag ((1 .. 12)) { - push @comps, "6551:1:${tag}"; - } - my $rpt_list = join q[;], @comps; - push @lims_list, - st::api::lims->new(%dr, batch_id => 12141, rpt_list => $rpt_list); - my $count = 0; - foreach my $lims (@lims_list) { - is($lims->rpt_list, $count ? $rpt_list : undef, 'rpt list value'); - is($lims->id_run, $count ? undef : 6551, 'id_run value'); - is($lims->position, $count ? undef : 1, 'position value'); - is($lims->lane_id(), $lims->rpt_list ? undef : 3065552, 'lane id'); - is($lims->batch_id, 12141, 'batch id'); - is($lims->is_control, 0, 'entity is not control'); - is($lims->is_pool, $lims->rpt_list ? undef : 1, 'pool flag value'); - is($lims->is_composition, $lims->rpt_list ? 1 : 0, 'composition flag value'); - - is($lims->library_id, $lims->rpt_list ? undef : 2988920, 'lib id'); - is($lims->library_name, $lims->rpt_list ? undef : '297p11', 'pool lib name'); - is($lims->seq_qc_state, $lims->rpt_list ? undef : 1, 'seq qc passed'); - is($lims->tag_sequence, undef, 'tag_sequence undefined'); - is(scalar keys %{$lims->tags}, $lims->rpt_list ? 12 : 13, '13 tags defined'); - is($lims->spiked_phix_tag_index, $lims->rpt_list ? undef : 168, - 'spiked phix tag index 168'); - if (!$lims->rpt_list) { - is($lims->tags->{$lims->spiked_phix_tag_index}, - 'ACAACGCAAT', 'tag_sequence for phix'); - } - is(scalar $lims->children, $lims->rpt_list ? 12 : 13, 'number of children'); - is($lims->num_children, $lims->rpt_list ? 12 : 13, 'number of children'); - - is($lims->sample_supplier_name, undef, 'supplier sample name undefined'); - is($lims->sample_cohort, undef, 'supplier sample cohort undefined'); - is($lims->sample_donor_id, undef, 'supplier sample donor id undefined'); - ok($lims->study_alignments_in_bam, 'alignment_in_bam is true'); - - my $plexes_hash = $lims->children_ia(); - my $k1 = $lims->rpt_list ? '6551:1:1' : 1; - my $k6 = $lims->rpt_list ? '6551:1:6' : 6; - my $p1 = $plexes_hash->{$k1}; - my $p6 = $plexes_hash->{$k6}; - is($p1->id_run, 6551, 'plex id_run'); - is($p1->position, 1, 'plex position'); - is($p1->tag_index, 1, 'plex tag index'); - ok(!$p1->is_pool, 'not a pool'); - ok(!$p1->is_composition, 'not a composition'); - is ($p1->default_tag_sequence, 'ATCACGTTAT', 'plex tag sequence'); - is($p1->sample_supplier_name, undef, 'supplier sample name undefined'); - is($p1->sample_cohort, undef, 'supplier sample cohort undefined'); - is($p1->sample_donor_id, undef, 'supplier sample donor id undefined'); - is ($p6->tag_index, 6, 'plex tag index'); - is ($p6->default_tag_sequence, 'GCCAATGTAT', 'plex tag sequence'); - - is($lims->to_string, $lims->rpt_list ? - "st::api::lims object, batch_id 12141, rpt_list $rpt_list" : - 'st::api::lims object, driver - xml, batch_id 12141, id_run 6551, position 1', - 'string respresentation of the object'); - - my @libs = @libs_6551_1; - my @samples = @samples_6551_1; - my @studies = @studies_6551_1; - if ($lims->rpt_list) { - shift @libs; - shift @samples; - shift @studies; - } - - is(join(q[,], $lims->library_names), join(q[,], sort @libs), - 'top level library_names list'); - is(join(q[,], $lims->sample_names), join(q[,], sort @samples), - 'top level sample_names list'); - is(join(q[,], $lims->sample_accession_numbers), join(q[,], sort @accessions_6551_1), - 'top level sample_accession_numbers list'); - is(join(q[,], $lims->study_names), join(q[,], sort @studies), - 'top level study_names list'); - - my $with_spiked_phix = 1; - my @lib_ids = qw/2798523 2798524 2798525 2798526 2798527 2798528 - 2798529 2798530 2798531 2798532 2798533 2798534/; - is_deeply([$lims->library_ids($with_spiked_phix)], - $lims->rpt_list ? [@lib_ids] : [2389196, @lib_ids], - 'top level library_ids list $with_spiked_phix = 1'); - is(join(q[,], $lims->library_names($with_spiked_phix)), join(q[,], sort @libs), - 'top level library_names list $with_spiked_phix = 1'); - - my @sample_ids = qw/1093818 1093819 1093820 1093821 1093822 1093823 - 1093824 1093825 1093826 1093827 1093828 1093829/; - is_deeply([$lims->sample_ids($with_spiked_phix)], - $lims->rpt_list ? [@sample_ids] : [@sample_ids, 1255141], - 'top level sample_names list $with_spiked_phix = 1'); - is(join(q[,], $lims->sample_names($with_spiked_phix)), join(q[,], sort @samples), - 'top level sample_names list $with_spiked_phix = 1'); - is(join(q[,], $lims->sample_accession_numbers($with_spiked_phix)), - join(q[,], sort @accessions_6551_1), - 'top level sample_accession_number list $with_spiked_phix = 1'); - - is(join(q[,], $lims->study_names($with_spiked_phix)), join(q[,], sort @studies), - 'top level study_names list $with_spiked_phix = 1'); - is(join(q[,], $lims->study_ids($with_spiked_phix)), - $lims->rpt_list ? '297' : '198,297', - 'top level study_ids list $with_spiked_phix = 1'); - is(join(q[,], $lims->project_ids($with_spiked_phix)), '297', - 'top level project_ids list $with_spiked_phix = 1'); - - $with_spiked_phix = 0; - if (!$lims->rpt_list) { - shift @libs; - shift @samples; - shift @studies; - } - is(join(q[,], $lims->library_names($with_spiked_phix)), join(q[,], sort @libs), - 'top level library_names list $with_spiked_phix = 0;'); - is(join(q[,], $lims->sample_names($with_spiked_phix)), join(q[,], sort @samples), - 'top level sample_names list $with_spiked_phix = 0;'); - is(join(q[,], $lims->sample_accession_numbers($with_spiked_phix)), - join(q[,], sort @accessions_6551_1), - 'top level sample_accession_number list $with_spiked_phix = 0'); - is(join(q[,], $lims->study_names($with_spiked_phix)), join(q[,], sort @studies), - 'top level study_names list $with_spiked_phix = 0;'); - is(join(q[,], $lims->library_types()), 'Standard', 'top level library types list'); - - is($lims->sample_consent_withdrawn, undef, 'consent withdrawn false'); - is($lims->any_sample_consent_withdrawn, 0, 'any consent withdrawn false'); - - $count++; - } -}; - -subtest 'Object for tag zero' => sub { - plan tests => 27; - - my $lims = st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 1, tag_index => 0); - is($lims->lane_id(), undef, q{lane_id undef for id_run 6551, position 1, tag_index defined} ); - is($lims->batch_id, 12141, 'batch id is 12141 for lane 1'); - is($lims->is_control, 0, 'lane 1 is not control'); - is($lims->is_pool, 1, 'lane 1 is pool'); - is($lims->library_id, 2988920, 'lib id'); - is($lims->library_name, '297p11', 'pool lib name'); - is($lims->contains_nonconsented_human, 0, 'does not contain nonconsented human'); - is($lims->contains_unconsented_human, 0, 'does not contain unconsented human (back compat)'); - is($lims->contains_nonconsented_xahuman, 0, 'does not contain nonconsented X and autosomal human'); - is($lims->tag_sequence, undef, 'tag_sequence undefined'); - is(scalar keys %{$lims->tags}, 13, '13 tags defined'); - is($lims->spiked_phix_tag_index, 168, 'spiked phix tag index'); - is(scalar $lims->descendants, 13, '13 descendant lims'); - is(scalar $lims->children, 13, '13 child lims'); - is($lims->to_string, 'st::api::lims object, driver - xml, batch_id 12141, id_run 6551, position 1, tag_index 0', 'object as string'); - is(join(q[,], $lims->library_names), join(q[,], sort @libs_6551_1), 'tag 0 library_names list'); - is(join(q[,], $lims->sample_names), join(q[,], sort @samples_6551_1), 'tag 0 sample_names list'); - is(join(q[,], $lims->sample_accession_numbers), join(q[,], sort @accessions_6551_1), 'tag 0 sample_accession_numbers list'); - is(join(q[,], $lims->study_names), join(q[,], sort @studies_6551_1), 'tag 0 study_names list'); - - my $with_spiked_phix = 1; - is(join(q[,], $lims->library_names($with_spiked_phix)), join(q[,], sort @libs_6551_1), 'tag 0 library_names list $with_spiked_phix = 1'); - is(join(q[,], $lims->sample_names($with_spiked_phix)), join(q[,], sort @samples_6551_1), 'tag 0 sample_names list $with_spiked_phix = 1'); - is(join(q[,], $lims->sample_accession_numbers($with_spiked_phix)), join(q[,], sort @accessions_6551_1), 'tag 0 sample_accession_numbers list $with_spiked_phix = 1'); - is(join(q[,], $lims->study_names($with_spiked_phix)), join(q[,], sort @studies_6551_1), 'tag 0 study_names list $with_spiked_phix = 1'); - - $with_spiked_phix = 0; - my @libs = @libs_6551_1; shift @libs; - my @samples = @samples_6551_1; shift @samples; - my @studies = @studies_6551_1; shift @studies; - is(join(q[,], $lims->library_names($with_spiked_phix)), join(q[,], sort @libs), 'tag 0 library_names list $with_spiked_phix = 0;'); - is(join(q[,], $lims->sample_names($with_spiked_phix)), join(q[,], sort @samples), 'tag 0 sample_names list $with_spiked_phix = 0;'); - is(join(q[,], $lims->sample_accession_numbers($with_spiked_phix)), join(q[,], sort @accessions_6551_1), 'tag 0 sample_accession_numbers list $with_spiked_phix = 0'); - is(join(q[,], $lims->study_names($with_spiked_phix)), join(q[,], sort @studies), 'tag 0 study_names list $with_spiked_phix = 0;'); -}; - -subtest 'Object for spiked phix tag' => sub { - plan tests => 24; - - my $lims = st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 1, tag_index => 168); - is($lims->is_control, 1, 'tag 1/168 is control'); - is($lims->is_pool, 0, 'tag 1/168 is not a pool'); - is($lims->contains_nonconsented_human, 0, 'does not contain nonconcented human'); - is($lims->contains_nonconsented_xahuman, 0, 'does not contain nonconsented X and autosomal human'); - my $lib_id = 2389196; - is($lims->library_id, $lib_id, 'hyb buffer lib id'); - my $lib_name = 'PhiX06Apr11'; - is($lims->library_name, $lib_name, 'hyb buffer lib name'); - my $sample_id = 1255141; - is($lims->sample_id, $sample_id, 'hyb buffer sample id'); - my $study_id = 198; - is($lims->study_id, $study_id, 'hyb buffer study id'); - is($lims->reference_genome, undef, 'reference genome not set'); - is($lims->tag_sequence, 'ACAACGCAAT', 'tag_sequence for phix'); - is($lims->tags, undef, 'tags undefined'); - is($lims->seq_qc_state, undef, 'no seq qc state'); - is($lims->spiked_phix_tag_index, 168, 'spiked phix tag index returned'); - is(scalar $lims->associated_lims, 0, 'no associated lims'); - is(scalar $lims->descendants, 0, 'no descendant lims'); - is(scalar $lims->associated_child_lims, 0, 'no associated child lims'); - is(scalar $lims->children, 0, 'no child lims'); - is(join(q[ ], $lims->library_names), $libs_6551_1[0], 'tag 168 library_names list'); - is(join(q[ ], $lims->sample_names), $samples_6551_1[0], 'tag 168 sample_names list'); - is(join(q[ ], $lims->sample_accession_numbers), q[], 'tag 168 sample_accession_numbers list (no accession for phiX)'); - is(join(q[ ], $lims->study_names), $studies_6551_1[0], 'tag 168 study_names list'); - - my $with_spiked_phix = 0; - is(join(q[ ], $lims->library_names($with_spiked_phix)), $libs_6551_1[0], 'tag 168 library_names list'); - is(join(q[ ], $lims->sample_names($with_spiked_phix)), $samples_6551_1[0], 'tag 168 sample_names list'); - is(join(q[ ], $lims->study_names($with_spiked_phix)), $studies_6551_1[0], 'tag 168 study_names list'); -}; - -subtest 'Object for a tag' => sub { - plan tests => 32; - - my $lims = st::api::lims->new( - %dr, id_run => 6551, batch_id => 12141, position => 1, tag_index => 1); - is($lims->is_control, 0, 'tag 1/1 is not control'); - is($lims->is_pool, 0, 'tag 1/1 is not a pool'); - is($lims->contains_nonconsented_human, 0, 'does not contain nonconcented human'); - is($lims->contains_nonconsented_xahuman, 0, 'does not contain nonconsented X and autosomal human'); - is($lims->spiked_phix_tag_index, 168, 'spiked phix tag index returned'); - is(join(q[ ], $lims->library_names), 'SS109305 2798523', 'tag 1 library_names list'); - is(join(q[ ], $lims->sample_names), 'SS109305', 'tag 1 sample_names list'); - is(join(q[ ], $lims->sample_accession_numbers), 'ERS024591', 'tag 1 sample_accession_numbers list'); - is(join(q[ ], $lims->study_names), $studies_6551_1[1], 'tag 1 study_names list'); - - my $with_spiked_phix = 0; - is(join(q[ ], $lims->library_names($with_spiked_phix)), 'SS109305 2798523', 'tag 1 library_names list $with_spiked_phix = 0'); - is(join(q[ ], $lims->sample_names($with_spiked_phix)), 'SS109305', 'tag 1 sample_names list $with_spiked_phix = 0'); - is(join(q[ ], $lims->sample_accession_numbers($with_spiked_phix)), 'ERS024591', 'tag 1 sample_accession_numbers list $with_spiked_phix = 0'); - is(join(q[ ], $lims->study_names($with_spiked_phix)), $studies_6551_1[1], 'tag 1 study_names list $with_spiked_phix = 0'); - - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5, tag_index => 1); - is($lims->batch_id, 12378, 'batch id for lane 5 tag 1'); - is($lims->tag_index, 1, 'tag index 1'); - is($lims->is_control, 0, 'plex 5/1 is not control'); - is($lims->is_pool, 0, 'plex 5/1 is not pool'); - is($lims->library_id, 3111679, 'lib id'); - is($lims->sample_id, 1132331, 'sample id'); - is($lims->study_id, 429, 'study id'); - is($lims->project_id, 429, 'project id'); - is($lims->request_id, undef, 'request id'); - is($lims->library_name, 'HiC_H_ON_DCJ 3111679', 'lib name'); - is($lims->sample_name, 'HiC_H_ON_DCJ', 'sample name undefined'); - is($lims->study_name, '3C and HiC of Plasmodium falciparum IT', 'study name'); - my $project_name = q[3C and HiC of Plasmodium falciparum IT]; - is($lims->project_name, $project_name, 'project name'); - is($lims->tag_sequence, 'ATCACGTT', 'tag_sequence'); - is($lims->tags, undef, 'tags undefined'); - is($lims->spiked_phix_tag_index, undef, 'spiked phix tag index undefined'); - ok(!$lims->alignments_in_bam, 'no bam alignment'); - is($lims->seq_qc_state, undef, 'no seq qc state'); - is(scalar $lims->associated_lims, 0, 'no associated lims'); -}; - -subtest 'Object for a non-pool lane' => sub { - plan tests => 99; - - my $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 1); - isa_ok($lims, 'st::api::lims'); - is($lims->batch_id, 12378, 'batch id for lane 1'); - is($lims->is_control, 0, 'lane 1 is not control'); - is($lims->is_pool, 0, 'lane 1 is not pool'); - is($lims->library_id, 3033734, 'lib id'); - is($lims->sample_id, 1121926, 'sample id'); - is($lims->study_id, 1811, 'study id'); - is($lims->project_id, 810, 'project id'); - is($lims->contains_nonconsented_human, 0, 'does not contain nonconcented human'); - is($lims->contains_nonconsented_xahuman, 0, 'does not contain nonconsented X and autosomal human'); - is($lims->request_id, 3156170, 'request id'); - is($lims->library_name, 'BS_3hrsomuleSm_202790 3033734', 'lib name'); - is($lims->sample_name, 'BS_3hrsomuleSm_202790', 'sample name'); - is($lims->study_name, 'Schistosoma mansoni methylome', 'study name'); - is($lims->project_name, 'Schistosoma mansoni methylome', 'project name'); - is($lims->tag_sequence, undef, 'tag_sequence undefined'); - is($lims->tags, undef, 'tags undefined'); - is($lims->spiked_phix_tag_index, undef, 'spiked phix tag index undefined'); - is($lims->tag_sequence, undef, 'tag_sequence undefined'); - is($lims->seq_qc_state, undef, 'seq qc not set'); - is(scalar $lims->associated_lims, 0, 'no associated lims'); - - my @methods; - lives_ok {@methods = $lims->method_list} 'list of attributes generated'; - foreach my $method (@methods) { - lives_ok {$lims->$method} qq[invoking method or attribute $method does not throw an error]; - } - - is(join(q[ ], $lims->library_names), 'BS_3hrsomuleSm_202790 3033734', 'non-pool lane library_names list'); - is(join(q[ ], $lims->sample_names), 'BS_3hrsomuleSm_202790', 'non-pool lane sample_names list'); - is(join(q[ ], $lims->sample_accession_numbers), 'ERS028649', 'non-pool lane sample_accession_numbers list'); - is(join(q[ ], $lims->study_names), 'Schistosoma mansoni methylome', 'non-pool lane study_names list'); -}; - -subtest 'Priority and seqqc state' => sub { - plan tests => 8; - - my $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 2); # non-pool lane - is($lims->seq_qc_state, undef, 'seq qc not set for pending'); - is($lims->lane_priority, 0, 'priority 0'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 3); - is($lims->seq_qc_state, 1, 'seq qc 1 for pass'); - is($lims->lane_priority, 1, 'priority 1'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 4); - is($lims->seq_qc_state, 0, 'seq qc 0 for fail'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5); - throws_ok {$lims->seq_qc_state} qr/Unexpected value 'some' for seq qc state/, - 'error for unexpected qc state'; - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5, tag_index => 1); - is($lims->lane_priority, undef, 'priority undefined on plex level'); - $lims = st::api::lims->new(%dr, id_run => 6607, batch_id => 12378); - is($lims->lane_priority, undef, 'priority undefined on batch level'); -}; - -subtest 'Object for a not spiked pool' => sub { - plan tests => 26; - - my $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5); - is($lims->batch_id, 12378, 'batch id for lane 5'); - is($lims->tag_index, undef, 'tag index undefined'); - is($lims->is_control, 0, 'lane 5 is not control'); - is($lims->is_pool, 1, 'lane 5 is pool'); - is($lims->library_id, 3111688, 'lib id'); - is($lims->sample_id, undef, 'sample id undefined'); - is($lims->study_id, 429, 'study id'); - is($lims->project_id, 429, 'project id'); - is($lims->request_id, 3259935, 'request id'); - is($lims->library_name, '3C_HiC_Pool3', 'lib name'); - is($lims->sample_name, undef, 'sample name undefined'); - is($lims->study_name, '3C and HiC of Plasmodium falciparum IT', 'study name'); - my $description = q[Illumina sequencing of chromatin conformation capture and its derivatives is being carried out to study nuclear architecture in antigenically selected lines of Plasmodium falciparum. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/]; - is($lims->study_description, $description, 'study description'); - is($lims->project_name, '3C and HiC of Plasmodium falciparum IT', 'project name'); - my $expected_tags = {1=>'ATCACGTT', 2=>'CGATGTTT', 3=>'TTAGGCAT', 4=>'TGACCACT', 5=>'ACAGTGGT', 6=>'GCCAATGT', 7=>'CAGATCTG', - 8 => 'ACTTGATG', 9=>'GATCAGCG',}; - is_deeply($lims->tags, $expected_tags, 'tags mapping'); - is($lims->spiked_phix_tag_index, undef, 'spiked phix tag index undefined'); - is($lims->tag_sequence, undef, 'tag_sequence undefined'); - is($lims->to_string, 'st::api::lims object, driver - xml, batch_id 12378, id_run 6607, position 5', 'object as string'); - - my $libs = 'HIC_M_B15C2 3111683,HiC_H_Dd2 3111680,HiC_H_LT3D7 3111687,HiC_H_OFF_DCJ 3111682,HiC_H_ON_DCJ 3111679,HiC_H_PQP1 3111681,HiC_M_3D7 3111685,HiC_M_ER3D7 3111686,HiC_M_Rev1 3111684'; - my $samples = 'HIC_M_B15C2,HiC_H_Dd2,HiC_H_LT3D7,HiC_H_OFF_DCJ,HiC_H_ON_DCJ,HiC_H_PQP1,HiC_M_3D7,HiC_M_ER3D7,HiC_M_Rev1'; - my $accessions = 'ERS033158,ERS033160,ERS033162,ERS033168,ERS033170,ERS033172,ERS033174,ERS033176,ERS033178'; - my $study = '3C and HiC of Plasmodium falciparum IT'; - is(join(q[,], $lims->library_names), $libs, 'pooled not-spiked lane library_names list'); - is(join(q[,], $lims->sample_names), $samples, 'pooled not-spiked lane sample_names list'); - is(join(q[,], $lims->sample_accession_numbers), $accessions, 'pooled not-spiked lane sample_accession_numbers list'); - is(join(q[,], $lims->study_names), $study, 'pooled not-spiked lane study_names list'); - - my $with_spiked_phix = 0; - is(join(q[,], $lims->library_names($with_spiked_phix)), $libs, 'pooled not-spiked lane library_names list $with_spiked_phix = 0'); - is(join(q[,], $lims->sample_names($with_spiked_phix)), $samples, 'pooled not-spiked lane sample_names list $with_spiked_phix = 0'); - is(join(q[,], $lims->sample_accession_numbers($with_spiked_phix)), $accessions, 'pooled not-spiked lane sample_accession_numbers list $with_spiked_phix = 0'); - is(join(q[,], $lims->study_names($with_spiked_phix)), $study, 'pooled not-spiked lane study_names list $with_spiked_phix = 0'); -}; - -{ - my $lims = st::api::lims->new(%dr, batch_id => 13410, position => 1); - ok(!$lims->is_control, 'lane is not a control (despite having a control tag within its hyb buffer tag)'); -} - -subtest 'Library types' => sub { - plan tests => 6; - - my $lims = st::api::lims->new(%dr, id_run => 6607, batch_id => 12378,); - is($lims->library_type, undef, 'library type undefined on a batch level'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 2); # non-pool lane - is($lims->library_type, 'Illumina cDNA protocol', 'library type'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5); - is($lims->library_type, undef, 'library type undefined for a pool'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5, tag_index => 0); - is($lims->library_type, undef, 'library type undefined for tag 0'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 5, tag_index => 1); - is($lims->library_type, 'Custom', 'library type'); - $lims = st::api::lims->new( - %dr, id_run => 6607, batch_id => 12378, position => 6, tag_index => 8); - is($lims->library_type, 'Standard', 'library type'); -}; - -subtest 'Unconcented human and xahuman' => sub { - plan tests => 11; - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/npg_api'; - - my $lims = st::api::lims->new(%dr, batch_id => 1536, position => 5); - ok(!$lims->is_pool, 'lane is not a pool'); - is($lims->contains_nonconsented_human, 1, 'contains nonconsented human'); - is($lims->contains_unconsented_human, 1, 'contains unconsented human (back compat)'); - - $lims = st::api::lims->new(%dr, batch_id => 13861, position => 2); - ok($lims->is_pool, 'lane is a pool'); - ok($lims->contains_nonconsented_human, 'pool contains unconsented human'); - - $lims = st::api::lims->new( - %dr, batch_id => 13861, position => 2, tag_index => 0); - ok($lims->contains_nonconsented_human, 'tag 0 contains unconsented human'); - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; - - $lims = st::api::lims->new(%dr, id_run => 8260, batch_id => 17763); - is($lims->contains_nonconsented_xahuman, 0, - 'run does contain nonconsented X and autosomal human does not propagate to run level'); - - $lims = st::api::lims->new( - %dr, id_run => 8260, batch_id => 17763, position => 2); - is($lims->contains_nonconsented_xahuman, 0, 'lane 2 does not contain nonconsented X and autosomal human'); - $lims = st::api::lims->new( - %dr, id_run => 8260, batch_id => 17763, position => 8); - is($lims->contains_nonconsented_xahuman, 1, 'lane 8 does contain nonconsented X and autosomal human'); - $lims = st::api::lims->new( - %dr, id_run => 8260, batch_id => 17763, position => 2, tag_index => 33); - is($lims->contains_nonconsented_xahuman, 0, 'plex 33 lane 2 does not contain nonconsented X and autosomal human'); - $lims = st::api::lims->new( - %dr, id_run => 8260, batch_id => 17763, position => 8, tag_index => 57); - is($lims->contains_nonconsented_xahuman, 1, 'plex 57 lane 8 does contain nonconsented X and autosomal human'); -}; - -subtest 'Bait name' => sub { - plan tests => 11; - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/npg_api'; - my $lims = st::api::lims->new(%dr, batch_id => 16442); - is($lims->bait_name, undef, 'bait name undefined on a batch level'); - $lims = st::api::lims->new(%dr, batch_id => 16442, position => 1); - is($lims->bait_name, undef, 'bait name undefined on a pool level'); - $lims = st::api::lims->new( - %dr, batch_id => 16442, position => 1, tag_index=> 2); - is($lims->bait_name,'Human all exon 50MB', 'bait name for a plex'); - $lims = st::api::lims->new( - %dr, batch_id => 16442, position => 1, tag_index=> 3); - is($lims->bait_name,'Fox bait', 'bait name for another plex'); - $lims = st::api::lims->new( - %dr, batch_id => 16442, position => 8, tag_index=> 5); - is($lims->bait_name,'Mouse some exon', 'bait name for yet another plex'); - $lims = st::api::lims->new( - %dr, batch_id => 16442, position => 1, tag_index=> 4); - is($lims->bait_name, undef, 'bait name undefined if no bait element'); - $lims = st::api::lims->new( - %dr, batch_id => 16442, position => 1, tag_index=> 5); - is($lims->bait_name, undef, 'bait name undefined if no bait name tag is empty'); - $lims = st::api::lims->new( - %dr, batch_id => 16442, position => 1, tag_index=> 168); - is($lims->bait_name, undef, 'bait name undefined for hyp buffer'); - - $lims = st::api::lims->new(%dr, batch_id => 3022, position => 1); - is($lims->bait_name,'Mouse all exon', 'bait name for a non-pool lane'); - $lims = st::api::lims->new(%dr, batch_id => 3022, position => 2); - is($lims->bait_name, undef, 'bait name undefined for a non-pool lane if there is no bait element'); - $lims = st::api::lims->new(%dr, batch_id => 3022, position => 4); - is($lims->bait_name, undef, 'bait name undefined for a control lane despite the presence of the bait element'); -}; - -subtest 'Study attributes' => sub { - plan tests => 11; - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; - - my $lims = st::api::lims->new(%dr, batch_id=>17763, position=>1,tag_index=>1); - is( $lims->study_title(), 'hifi test', q{study title} ); - is( $lims->study_name(), 'Kapa HiFi test', 'study name'); - is( $lims->study_accession_number(), undef, q{no study accession obtained} ); - is( $lims->study_publishable_name(), q{hifi test}, q{study title returned as publishable name} ); - - $lims = st::api::lims->new(%dr, batch_id=>17763, position=>1,tag_index=>2); - ok(! $lims->alignments_in_bam, 'no alignments in BAM when false in corresponding XML in study'); - is( $lims->study_title(), 'Genetic variation in Kuusamo', q{study title obtained} ); - is( $lims->study_accession_number(), 'EGAS00001000020', q{study accession obtained} ); - is( $lims->study_publishable_name(), 'EGAS00001000020', q{accession returned as study publishable name} ); - is( $lims->sample_publishable_name(), q{ERS003242}, q{sample publishable name returns accession} ); - ok(! $lims->separate_y_chromosome_data, 'do not separate y chromosome data'); - - $lims = st::api::lims->new(%dr, batch_id => 22061, position =>1, tag_index=>66); - ok($lims->separate_y_chromosome_data, 'separate y chromosome data'); -}; - -subtest 'Tag sequence and library type from sample description' => sub { - plan tests => 15; - - my $sample_description = 'AB GO (grandmother) of the MGH meiotic cross. The same DNA was split into three aliquots (of which this'; - is(st::api::lims::_tag_sequence_from_sample_description($sample_description), undef, q{tag undefined for a description containing characters in round brackets} ); - $sample_description = "3' end enriched mRNA from morphologically abnormal embryos from dag1 knockout incross 3. A 6 base indexing sequence (GTAGAC) is bases 5 to 11 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD"; - is(st::api::lims::_tag_sequence_from_sample_description($sample_description), q{GTAGAC}, q{correct tag from a complex description} ); - $sample_description = "^M"; - is(st::api::lims::_tag_sequence_from_sample_description($sample_description), undef, q{tag undefined for a description with carriage return} ); - - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/tag_from_sample_description'; - #diag q[Tests for deducing tags from batch 19158 (associated with run 3905 by hand)]; - my $lims8 = st::api::lims->new(%dr, batch_id => 19158, position => 8); - my @alims8 = $lims8->associated_lims; - is(scalar @alims8, 7, 'Found 7 plexes in position 8'); - - my @tags = $lims8->tags(); - is(scalar @tags, 1, 'Found 1 tags array'); - - cmp_ok($tags[0]->{5}, q(ne), q(ACAGTGGT), 'Do not use expected_sequence sequence for tag'); - cmp_ok($tags[0]->{5}, q(eq), q(GTAGAC), 'Use sample_description sequence for tag'); - - my $lims1 = st::api::lims->new(%dr, batch_id => 19158, position => 1); - my @alims1 = $lims1->associated_lims; - is(scalar @alims1, 6, 'Found 6 plexes in position 1'); - - my @tags1 = $lims1->tags(); - is(scalar @tags1, 1, 'Found 1 tags array'); - - cmp_ok($tags1[0]->{144}, q(eq), q(CCTGAGCA), 'Use expected_sequence sequence for tag'); - - my $lims85 = st::api::lims->new( - %dr, batch_id => 19158, position => 8, tag_index => 5); - is($lims85->library_type, '3 prime poly-A pulldown', 'library type'); - is($lims85->tag_sequence, 'GTAGAC', 'plex tag sequence from sample description'); - ok($lims85->sample_description =~ /end enriched mRNA/sm, 'sample description available'); - - my $lims1144 = st::api::lims->new( - %dr, batch_id => 19158, position => 1, tag_index => 144); - isnt($lims1144->library_type, '3 prime poly-A pulldown', 'library type'); - is($lims1144->tag_sequence, 'CCTGAGCA', 'plex tag sequence directly from batch xml'); -}; - -subtest 'Inline index' => sub { - plan tests => 14; - - my $lims = st::api::lims->new( - %dr, id_run=>10638, batch_id=>22829, position=>5); - is ($lims->id_run(), 10638, "Found the run"); - my @children = $lims->children(); - isnt (scalar @children, 0, "We have children"); - is($lims->inline_index_exists,1,'Found an inline index'); - is($lims->inline_index_start,7,'found correct inline index start'); - is($lims->inline_index_end,12,'found correct inline index end'); - is($lims->inline_index_read,2,'found correct inline index read'); - is($lims->tag_sequence,undef,'tag sequence undefined for lane level'); - - $lims = st::api::lims->new( - %dr, id_run=>10638, batch_id=>22829, position=>6); - is ($lims->id_run(), 10638, "Found the run"); - @children = $lims->children(); - isnt (scalar @children, 0, "We have children"); - is($lims->inline_index_exists,1,'Found an inline index'); - is($lims->inline_index_start,6,'found correct inline index start'); - is($lims->inline_index_end,10,'found correct inline index end'); - is($lims->inline_index_read,1,'found correct inline index read'); - is($lims->tag_sequence,undef,'tag sequence undefined for lane level'); -}; - subtest 'Run-level object via samplesheet driver' => sub { plan tests => 36; @@ -806,42 +191,31 @@ subtest 'Run-level object via samplesheet driver' => sub { }; subtest 'Lane-level object via samplesheet driver' => sub { - plan tests => 16; + plan tests => 14; my $path = 't/data/samplesheet/miseq_default.csv'; lives_ok {st::api::lims->new(id_run => 10262, position =>2, path => $path, driver_type => 'samplesheet')} 'no error instantiation an object for a non-existing lane'; throws_ok {st::api::lims->new(id_run => 10262, position =>2, path => $path, driver_type => 'samplesheet')->library_id} qr/Position 2 not defined in/, 'error invoking a driver method on an object for a non-existing lane'; - lives_ok {st::api::lims->new(id_run => 10262, position =>2, driver_type => 'samplesheet')} 'no error instantiation an object without path'; - throws_ok {st::api::lims->new(id_run => 10262, position =>2, driver_type => 'samplesheet')->library_id} - qr/Attribute \(path\) does not pass the type constraint/, 'error invoking a driver method on an object with path undefined'; # NPG_CACHED_SAMPLESHEET_FILE is unset - - my $nopath = join q[/], tempdir( CLEANUP => 1 ), 'xxx'; - throws_ok {st::api::lims->new(id_run => 10262, path => $nopath, position =>2, driver_type => 'samplesheet')->library_id} - qr/Validation failed for 'NpgTrackingReadableFile'/, 'error invoking a driver method on an object with non-existing path'; - - { - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $path; - - my $ss=st::api::lims->new(id_run => 10262, position =>1, driver_type => 'samplesheet'); - is ($ss->path, $path, 'samplesheet path captured from NPG_CACHED_SAMPLESHEET_FILE') or diag explain $ss; - is ($ss->position, 1, 'correct position'); - is ($ss->is_pool, 1, 'lane is a pool'); - is ($ss->library_id, undef, 'pool lane library_id undefined'); - is (scalar $ss->children, 96, '96 plexes returned'); - } - - my $ss=st::api::lims->new(id_run => 10262, position =>1, tag_index => 0, path => $path, driver_type => 'samplesheet'); + my $ss=st::api::lims->new(id_run => 10262, position =>1, tag_index => 0, path => $path); is (scalar $ss->children, 96, '96 children returned for tag zero'); is ($ss->is_pool, 1, 'tag zero is a pool'); is ($ss->library_id, undef, 'tag_zero library_id undefined'); is ($ss->default_tag_sequence, undef, 'default tag sequence undefined'); is ($ss->tag_sequence, undef, 'tag sequence undefined'); is ($ss->purpose, undef, 'purpose'); + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $path; + $ss=st::api::lims->new(id_run => 10262, position =>1); + is ($ss->path, $path, 'samplesheet path captured from NPG_CACHED_SAMPLESHEET_FILE') or diag explain $ss; + is ($ss->position, 1, 'correct position'); + is ($ss->is_pool, 1, 'lane is a pool'); + is ($ss->library_id, undef, 'pool lane library_id undefined'); + is (scalar $ss->children, 96, '96 plexes returned'); }; subtest 'Plex-level object via samplesheet driver' => sub { @@ -959,75 +333,7 @@ subtest 'Samplesheet driver for arbitrary compositions' => sub { is ($ss->tag_index, 4, 'correct tag_index'); }; -subtest 'Instantiating a samplesheet driver' => sub { - plan tests => 16; - - my $ss_path = 't/data/samplesheet/miseq_default.csv'; - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $ss_path; - my $l; - lives_ok {$l = st::api::lims->new(id_run => 10262,)} - 'no error creating an object with samplesheet file defined in env var'; - is ($l->driver_type, 'samplesheet', 'driver type is built as samplesheet'); - is ($l->path, $ss_path, 'correct path is built'); - is (ref $l->driver, 'st::api::lims::samplesheet', 'correct driver object type'); - is ($l->driver->path, $ss_path, 'correct path assigned to the driver object'); - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet'; - ok (-d $ENV{NPG_CACHED_SAMPLESHEET_FILE}); - lives_ok {$l = st::api::lims->new(id_run => 10262,)} - 'no error creating an object with samplesheet file defined in env var'; - is ($l->driver_type, 'samplesheet', 'driver type is samplesheet'); - throws_ok { $l->path } - qr/Attribute \(path\) does not pass the type constraint/, - 'samplesheet cannot be a directory'; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/non-existing'; - ok (not -e $ENV{NPG_CACHED_SAMPLESHEET_FILE}); - lives_ok {$l = st::api::lims->new(id_run => 10262,)} - 'no error creating an object with samplesheet file defined in env var'; - is ($l->driver_type, 'samplesheet', 'driver type is samplesheet'); - throws_ok {$l->children} - qr/Attribute \(path\) does not pass the type constraint/, - 'samplesheet file should exist'; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/non-existing'; - lives_ok {$l = st::api::lims->new(id_run => 10262, path => $ss_path)} - 'no error creating an object with samplesheet file defined in env var and path given'; - is ($l->driver_type, 'samplesheet', 'driver type is samplesheet'); - lives_ok {$l->children} 'given path takes precedence'; -}; - -subtest 'Dual index' => sub { - plan tests => 16; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/dual_index_extended.csv'; - my $l = st::api::lims->new(id_run => 6946); - my @lanes = $l->children; - is (scalar @lanes, 2, 'two lanes'); - my @plexes = $lanes[0]->children; - is (scalar @plexes, 3, 'three samples in lane 1'); - my $plex = $plexes[0]; - is($plex->default_tag_sequence, 'CGATGTTT', 'first index'); - is($plex->default_tagtwo_sequence, 'AAAAAAAA', 'second index'); - is($plex->tag_sequence, 'CGATGTTTAAAAAAAA', 'combined tag sequence'); - $plex = $plexes[2]; - is($plex->default_tag_sequence, 'TGACCACT', 'first index'); - is($plex->default_tagtwo_sequence, 'AAAAAAAA', 'second index'); - is($plex->tag_sequence, 'TGACCACTAAAAAAAA', 'combined tag sequence'); - @plexes = $lanes[1]->children; - is (scalar @plexes, 3, 'three samples in lane 2'); - $plex = $plexes[0]; - is($plex->default_tag_sequence, 'GCTAACTC', 'first index'); - is($plex->default_tagtwo_sequence, 'GGGGGGGG', 'second index'); - is($plex->tag_sequence, 'GCTAACTCGGGGGGGG', 'combined tag sequence'); - $plex = $plexes[2]; - is($plex->default_tag_sequence, 'GTCTTGGC', 'first index'); - is($plex->default_tagtwo_sequence, 'GGGGGGGG', 'second index'); - is($plex->tag_sequence, 'GTCTTGGCGGGGGGGG', 'combined tag sequence'); - is($plex->purpose, 'standard', 'purpose'); -}; - -subtest 'aggregation across lanes for pools' => sub { +subtest 'Aggregation across lanes for pools' => sub { plan tests => 85; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; @@ -1205,7 +511,7 @@ subtest 'aggregation across lanes for pools' => sub { 'sample names including spiked phix'); }; -subtest 'aggregation across lanes for non-pools' => sub { +subtest 'Aggregation across lanes for non-pools' => sub { plan tests => 13; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_rapidrun_nopool.csv'; @@ -1240,7 +546,30 @@ subtest 'aggregation across lanes for non-pools' => sub { } }; -subtest 'creating tag zero object' => sub { +subtest 'Aggregation across lanes for a tag' => sub { + plan tests => 13; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + + my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1'); + + my $e = qr/id_run and position are expected as arguments/; + throws_ok { $l->create_lane_object() } $e, 'no arguments - error'; + throws_ok { $l->create_lane_object(1) } $e, 'one argument - error'; + throws_ok { $l->create_lane_object(1, 0) } $e, + 'one of argument is false - error'; + + for my $p ((1,2)) { + my $lane_l = $l->create_lane_object(25846, $p); + is ($lane_l->id_run, 25846, 'run id is 25846'); + is ($lane_l->position, $p, "position is $p"); + is ($lane_l->rpt_list, undef, 'rpt_list is undefined'); + is ($lane_l->tag_index, undef, 'tag index is undefined'); + ok ($lane_l->is_pool, 'the entity is a pool'); + } +}; + +subtest 'Creating tag zero object' => sub { plan tests => 4; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; @@ -1260,27 +589,232 @@ subtest 'creating tag zero object' => sub { is ($l->create_tag_zero_object()->to_string(), $description, 'created from plex-level object'); }; -subtest 'creating lane object' => sub { - plan tests => 13; +subtest 'Dual index' => sub { + plan tests => 16; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/dual_index_extended.csv'; + my $l = st::api::lims->new(id_run => 6946); + my @lanes = $l->children; + is (scalar @lanes, 2, 'two lanes'); + my @plexes = $lanes[0]->children; + is (scalar @plexes, 3, 'three samples in lane 1'); + my $plex = $plexes[0]; + is($plex->default_tag_sequence, 'CGATGTTT', 'first index'); + is($plex->default_tagtwo_sequence, 'AAAAAAAA', 'second index'); + is($plex->tag_sequence, 'CGATGTTTAAAAAAAA', 'combined tag sequence'); + $plex = $plexes[2]; + is($plex->default_tag_sequence, 'TGACCACT', 'first index'); + is($plex->default_tagtwo_sequence, 'AAAAAAAA', 'second index'); + is($plex->tag_sequence, 'TGACCACTAAAAAAAA', 'combined tag sequence'); + @plexes = $lanes[1]->children; + is (scalar @plexes, 3, 'three samples in lane 2'); + $plex = $plexes[0]; + is($plex->default_tag_sequence, 'GCTAACTC', 'first index'); + is($plex->default_tagtwo_sequence, 'GGGGGGGG', 'second index'); + is($plex->tag_sequence, 'GCTAACTCGGGGGGGG', 'combined tag sequence'); + $plex = $plexes[2]; + is($plex->default_tag_sequence, 'GTCTTGGC', 'first index'); + is($plex->default_tagtwo_sequence, 'GGGGGGGG', 'second index'); + is($plex->tag_sequence, 'GTCTTGGCGGGGGGGG', 'combined tag sequence'); + is($plex->purpose, 'standard', 'purpose'); +}; + +subtest 'Insert size' => sub { + plan tests => 14; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/4pool4libs_extended.csv'; + + my $lims = st::api::lims->new(id_run => 9999); + is_deeply($lims->required_insert_size, {}, 'no insert size on run level'); + + $lims = st::api::lims->new(id_run => 9999, position => 1); + my $id = $lims->library_id; + my $insert_size = $lims->required_insert_size; + is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); + is ($insert_size->{$id}->{q[from]}, 400, 'required FROM insert size'); + is ($insert_size->{$id}->{q[to]}, 550, 'required TO insert size'); + + $lims = st::api::lims->new(id_run => 9999, position => 7); + ok ($lims->is_pool, 'lane is a pool'); + $insert_size = $lims->required_insert_size; + is (keys %{$insert_size}, 2, 'two entries in the insert size hash'); + $id = '8324594'; + is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size'); + is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size'); + $id = '8324595'; + is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size'); + is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size'); + ok (!exists $insert_size->{q[6946_7_ACAACGCAAT]}, 'no required insert size'); + + $lims = st::api::lims->new(id_run => 9999, position => 7, tag_index => 77); + $insert_size = $lims->required_insert_size; + is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); + is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size'); + is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size'); +}; + +subtest 'Study and sample properties' => sub { + plan tests => 12; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/4pool4libs_extended.csv'; + + my $lims = st::api::lims->new(id_run => 9999, position => 1); + is( $lims->study_title(), 'Haemonchus contortus Ivermectin Resistance', + 'study title' ); + is( $lims->study_name(), 'Haemonchus contortus Ivermectin Resistance', + 'study name'); + is( $lims->study_accession_number(), 'ERP000430', 'study accession number'); + is( $lims->study_publishable_name(), 'ERP000430', + 'study accession number returned as publishable name'); + ok( !$lims->alignments_in_bam, 'no alignments'); + + $lims = st::api::lims->new(id_run => 9999, position => 7, tag_index=> 76); + ok($lims->alignments_in_bam, 'do alignments'); + like( $lims->study_title(), + qr/Mouse model to quantify genotype-epigenotype variations /, + 'study title'); + is( $lims->study_name(), + 'Mouse model to quantify genotype-epigenotype variations_RNA', + 'study name'); + is( $lims->study_publishable_name(), 'ERP002223', + 'accession is returned as study publishable name'); + is( $lims->sample_publishable_name(), 'ERS354534', + 'sample publishable name returns accession'); + ok(!$lims->separate_y_chromosome_data, 'do not separate y chromosome data'); + + $lims = st::api::lims->new(id_run => 9999, position => 7); + is( $lims->study_name(), + 'Mouse model to quantify genotype-epigenotype variations_RNA', + 'study name'); +}; + +subtest 'Bait name' => sub { + plan tests => 8; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/samplesheet_7753.csv'; + + my $lims = st::api::lims->new(id_run => 7753); + is($lims->bait_name, undef, 'bait name undefined on run level'); + $lims = st::api::lims->new(id_run => 7753, position => 1); + is($lims->bait_name, undef, 'bait name undefined on a pool level'); + $lims = st::api::lims->new(id_run => 7753, position => 1, tag_index=> 2); + is($lims->bait_name,'Human all exon 50MB', 'bait name for a plex'); + $lims = st::api::lims->new(id_run => 7753, position => 1, tag_index=> 3); + is($lims->bait_name, 'Human all exon 50MB', + 'bait name with white space around it'); + $lims = st::api::lims->new(id_run => 7753, position => 1, tag_index=> 5); + is($lims->bait_name, undef, 'all white space bait name'); + $lims = st::api::lims->new(id_run => 7753, position => 2, tag_index=> 1); + is($lims->bait_name, undef, 'no bait name'); + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/4pool4libs_extended.csv'; + + $lims = st::api::lims->new(id_run => 9999, position => 1); + is($lims->bait_name, undef, + 'bait name undefined for a non-pool lane if there is no bait element'); + $lims = st::api::lims->new(id_run => 9999, position => 2); + is($lims->bait_name,'Fox bait', 'bait name for a non-pool lane'); +}; + +subtest 'Consent and separation of human data' => sub { + plan tests => 17; + + my $schema_wh; + lives_ok { $schema_wh = Moose::Meta::Class->create_anon_class( + roles => [qw/npg_testing::db/])->new_object({})->create_test_db( + q[WTSI::DNAP::Warehouse::Schema],q[t/data/fixtures_lims_wh_samplesheet]) + } 'ml_warehouse test db created'; + + my $lims = st::api::lims->new( + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + id_flowcell_lims => 13994, + position => 1, + tag_index => 4 + ); + is( $lims->sample_consent_withdrawn, 1, 'sample consent is withdrawn'); + + $lims = st::api::lims->new( + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + id_flowcell_lims => 13994, + position => 1, + tag_index => 5 + ); + is( $lims->sample_consent_withdrawn, 0, 'sample consent is not withdrawn'); + + $lims = st::api::lims->new( + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + id_flowcell_lims => 13994, + position => 1, + ); + ok( $lims->is_pool, 'lane is a pool'); + ok( $lims->contains_nonconsented_human, 'lane contains unconsented human'); + ok( $lims->separate_y_chromosome_data, 'Y chromosome should be separated'); + ok( $lims->contains_nonconsented_xahuman, + 'lane does contain nonconsented X and autosomal human'); - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + $lims = st::api::lims->new( + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + id_flowcell_lims => 13994, + position => 1, + tag_index => 0 + ); + ok( $lims->contains_nonconsented_human, 'tag0 contains unconsented human'); + ok( $lims->separate_y_chromosome_data, 'tag0 Y chromosome should be separated'); + ok( $lims->contains_nonconsented_xahuman, + 'tag0 does contain nonconsented X and autosomal human'); - my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1'); + $lims = st::api::lims->new( + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + id_flowcell_lims => 13994 + ); + ok( !$lims->contains_nonconsented_human, + 'unconsented human flag does not propagate to the batch level'); + ok( !$lims->separate_y_chromosome_data, + 'Y chromosome separation flag does not propagate to the batch level'); + ok( !$lims->contains_nonconsented_xahuman, + 'nonconsented X and autosomal human flag does not propagate to the batch level'); - my $e = qr/id_run and position are expected as arguments/; - throws_ok { $l->create_lane_object() } $e, 'no arguments - error'; - throws_ok { $l->create_lane_object(1) } $e, 'one argument - error'; - throws_ok { $l->create_lane_object(1, 0) } $e, - 'one of argument is false - error'; + $lims = st::api::lims->new( + driver_type => 'ml_warehouse', + mlwh_schema => $schema_wh, + id_flowcell_lims => 76873, + position => 1, + ); + ok( $lims->is_pool, 'lane is a pool'); + ok( !$lims->contains_nonconsented_human, + 'lane does not contain unconsented human'); + ok( !$lims->separate_y_chromosome_data, 'Y chromosome should not be separated'); + ok( !$lims->contains_nonconsented_xahuman, + 'lane does not contain nonconsented X and autosomal human'); +}; - for my $p ((1,2)) { - my $lane_l = $l->create_lane_object(25846, $p); - is ($lane_l->id_run, 25846, 'run id is 25846'); - is ($lane_l->position, $p, "position is $p"); - is ($lane_l->rpt_list, undef, 'rpt_list is undefined'); - is ($lane_l->tag_index, undef, 'tag index is undefined'); - ok ($lane_l->is_pool, 'the entity is a pool'); - } +subtest 'Library types' => sub { + plan tests => 6; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/4pool4libs_extended.csv'; + + my $lims = st::api::lims->new(id_run => 9999); + is($lims->library_type, undef, 'library type undefined on a batch level'); + $lims = st::api::lims->new(id_run => 9999, position => 2); # non-pool lane + is($lims->library_type, 'No PCR', 'library type'); + $lims = st::api::lims->new(id_run => 9999, position => 8); + is($lims->library_type, undef, 'library type undefined for a pool'); + $lims = st::api::lims->new(id_run => 9999, position => 8, tag_index => 0); + is($lims->library_type, undef, 'library type undefined for tag 0'); + $lims = st::api::lims->new(id_run => 9999, position => 8, tag_index => 88); + is($lims->library_type, 'Pre-quality controlled', 'library type'); + $lims = st::api::lims->new(id_run => 9999, position => 8, tag_index => 168); + is($lims->library_type, undef, 'library type is not specified'); }; 1; diff --git a/t/45-st-api-lims-traversal.t b/t/45-st-api-lims-traversal.t deleted file mode 100644 index 981d50a0..00000000 --- a/t/45-st-api-lims-traversal.t +++ /dev/null @@ -1,111 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 41; -use Test::Deep; -use Test::Exception; -use Try::Tiny; - -sub _positions { - my @lims = @_; - my @positions = (); - foreach my $lims (@lims) { - if (!defined $lims->tag_index) { - push @positions, $lims->position; - } - } - return sort @positions; -} - -use_ok('st::api::lims'); - -foreach my $pa ((['using mocked data', q[t/data/test45], 'xml'])) -{ - my $do_test = 1; - my $reason = q[]; - my $driver = $pa->[2]; - my $test_data_dir = $pa->[1]; - diag($pa->[0], ", $driver driver"); - local $ENV{NPG_WEBSERVICE_CACHE_DIR} = $test_data_dir; - my $lfield = 'batch_id'; - - { - my $lims = st::api::lims->new($lfield => 4775, driver_type => $driver); - isa_ok($lims, 'st::api::lims', 'lims isa'); - my @alims = $lims->associated_lims; - is(scalar @alims, 8, '8 associated lims objects'); - my @positions = _positions(@alims); - is(scalar @positions, 8, '8 lanes in a batch'); - is(join(q[ ],@positions), '1 2 3 4 5 6 7 8', 'all positions'); - - my $lims1 = st::api::lims->new($lfield => 4775, position => 1, driver_type => $driver); - is($lims1->is_control, 0, 'first st lane has no control'); - is($lims1->is_pool, 0, 'first st lane has no pool'); - is(scalar $lims1->associated_lims, 0, 'no associated lims for a lane'); - cmp_ok($lims1->library_id, q(==), 57440, 'lib id from first st lane'); - my $expected_name = $driver eq 'xml' ? 'PD3918a 1' : '57440'; - cmp_ok($lims1->library_name, q(eq), $expected_name, 'lib name from first st lane'); - - my $insert_size; - lives_ok {$insert_size = $lims1->required_insert_size} 'insert size for the first lane'; - is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); - is ($insert_size->{$lims1->library_id}->{q[from]}, 300, 'required FROM insert size'); - is ($insert_size->{$lims1->library_id}->{q[to]}, 400, 'required TO insert size'); - - ok(!$lims1->sample_consent_withdrawn(), 'sample consent not withdrawn'); - ok(!$lims1->any_sample_consent_withdrawn(), 'not any sample consent withdrawn'); - - my $lims4 = st::api::lims->new($lfield => 4775, position => 4, driver_type => $driver); - is($lims4->is_control, 1, 'first st lane has control'); - is($lims4->is_pool, 0, 'first st lane has no pool'); - cmp_ok($lims4->library_id, q(==), 79577, 'control id from fourth st lane'); - if ($driver eq 'xml') { - cmp_ok($lims4->library_name, q(eq), 'phiX CT1462-2 1', 'control name from fourth st lane'); - } else { - cmp_ok($lims4->library_name, q(==), 79577, 'control library id from fourth st lane'); - } - cmp_ok($lims4->sample_id, q(==), 9836, 'sample id from fourth st lane'); - ok(!$lims4->study_id, 'study id from fourth st lane undef'); - ok(!$lims4->project_id, 'project id from fourth st lane undef'); - my $request_id = $lims4->request_id; - $request_id ||= 0; - my $expected_request_id = $driver eq 'xml' ? 43779 : 0; - cmp_ok($request_id, q(==), $expected_request_id, 'request id from fourth st lane'); - is_deeply($lims4->required_insert_size, {}, 'no insert size for control lane'); - - my $lims6 = st::api::lims->new($lfield => 4775, position => 6, driver_type => $driver); - is($lims6->study_id, 333, 'study id'); - cmp_ok($lims6->study_name, q(eq), q(CLL whole genome), 'study name'); - - cmp_bag($lims6->email_addresses,[qw(dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk sm2@sanger.ac.uk)],'All email addresses'); - cmp_bag($lims6->email_addresses_of_managers,[qw(sm2@sanger.ac.uk)],'Managers email addresses'); - is_deeply($lims6->email_addresses_of_followers,[qw(dg10@sanger.ac.uk las@sanger.ac.uk pc8@sanger.ac.uk)],'Followers email addresses'); - is_deeply($lims6->email_addresses_of_owners,[qw(sm2@sanger.ac.uk)],'Owners email addresses'); - - is($lims6->alignments_in_bam, 1,'do bam alignments'); - - my $lims7 = st::api::lims->new($lfield => 16249, position => 1, driver_type => $driver); - is($lims7->reference_genome, 'Homo_sapiens (1000Genomes)', - 'reference genome when common for whole pool'); - is($lims7->bait_name, 'Human all exon 50MB', 'bait name when common for whole pool'); - $lims7 = st::api::lims->new($lfield => 16249, position => 1, tag_index => 2, driver_type => $driver); - is($lims7->bait_name, 'Human all exon 50MB', 'bait name for a plex'); - $lims7 = st::api::lims->new($lfield => 16249, position => 1, tag_index => 168, driver_type => $driver); - is($lims7->bait_name, undef, 'bait name undefined for spiked phix plex'); - - $lims7 = st::api::lims->new($lfield => 16249, position => 1, tag_index => 0, driver_type => $driver); - is($lims7->reference_genome, 'Homo_sapiens (1000Genomes)', - 'tag zero reference genome when common for whole pool'); - my $lims8 = st::api::lims->new($lfield =>15728, position=>2, tag_index=>3, driver_type => $driver); - ok( $lims8->sample_consent_withdrawn(), 'sample 1299723 consent withdrawn' ); - ok( $lims8->any_sample_consent_withdrawn(), 'any sample (1299723) consent withdrawn' ); - - my $lims9 = st::api::lims->new($lfield =>15728, position=>2, tag_index=>0, driver_type => $driver); - ok( $lims9->any_sample_consent_withdrawn(), 'any sample consent withdrawn' ); - - my $lims10 = st::api::lims->new($lfield =>43500, position=>1, tag_index=>1, driver_type => $driver); - is($lims10->purpose,'standard','Purpose'); - - } -} - -1; diff --git a/t/47-samplesheet.t b/t/47-samplesheet.t index d27e1f7f..a74dc5fc 100644 --- a/t/47-samplesheet.t +++ b/t/47-samplesheet.t @@ -9,7 +9,7 @@ use File::Path qw/make_path/; use Moose::Meta::Class; use t::dbic_util; -local $ENV{'dev'} = q(wibble); # ensure we're not going live anywhere +local $ENV{'dev'} = q(wibble); local $ENV{'HOME'} = q(t/); use_ok('npg::samplesheet'); diff --git a/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml b/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml index 95a25c9e..43083182 100644 --- a/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml +++ b/t/data/fixtures_lims_wh_samplesheet/000-Sample.yml @@ -258,7 +258,7 @@ common_name: Human compound: ~ concentration_determined_by: ~ - consent_withdrawn: 0 + consent_withdrawn: 1 control: ~ control_type: ~ country_of_origin: ~ diff --git a/t/data/fixtures_lims_wh_samplesheet/000-Study.yml b/t/data/fixtures_lims_wh_samplesheet/000-Study.yml index efefbef2..c02fdfa6 100644 --- a/t/data/fixtures_lims_wh_samplesheet/000-Study.yml +++ b/t/data/fixtures_lims_wh_samplesheet/000-Study.yml @@ -85,7 +85,7 @@ aligned: 1 array_express_accession_number: ~ contains_human_dna: 0 - contaminated_human_dna: 0 + contaminated_human_dna: 1 created: 2010-10-07 15:11:00 data_access_group: ~ data_deletion_period: ~ @@ -111,9 +111,9 @@ prelim_id: ~ recorded_at: 2021-10-15 08:54:47 reference_genome: ' ' - remove_x_and_autosomes: 0 + remove_x_and_autosomes: 1 s3_email_list: ~ - separate_y_chromosome_data: 0 + separate_y_chromosome_data: 1 state: active study_title: hifi test study_type: Whole Genome Sequencing diff --git a/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml b/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml index 3313f624..149e7c02 100644 --- a/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml +++ b/t/data/fixtures_lims_wh_samplesheet/100-IseqFlowcell.yml @@ -859,7 +859,7 @@ tag_set_name: 'Sanger_168tags - 10 mer tags' team: Illumina-C workflow: ~ -- bait_name: ~ +- bait_name: Fox bait cost_code: S0702 entity_id_lims: 8381744 entity_type: library diff --git a/t/data/samplesheet/4pool4libs_extended.csv b/t/data/samplesheet/4pool4libs_extended.csv index d3d3d0d3..e7392dc6 100644 --- a/t/data/samplesheet/4pool4libs_extended.csv +++ b/t/data/samplesheet/4pool4libs_extended.csv @@ -1,7 +1,7 @@ [Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, 1,7809257,ERS323818,,,,,No PCR,,,,,,,,0,0,8381746,0,7809257,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323818,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660679,,Hc_4_BC4_P2_5046_340285,Haemonchus contortus MHco3%2F4.BC4(P2)-5046,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, -2,7809258,ERS323819,,,,,No PCR,,,,,,,,0,0,8381744,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +2,7809258,ERS323819,,,,Fox bait,No PCR,,,,,,,,0,0,8381744,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, 3,7809258,ERS323819,,,,,No PCR,,,,,,,,0,0,8381745,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, 4,8215019,ERS351213,,TAAGGCGA,TAGATCGC,,qPCR only,TAAGGCGATAGATCGC,,,,,,,0,0,8381739,0,8215019,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351213,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706390,,mES_ai2_s2_cell1,mES_ai2_s2_cell1,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,1, 4,8215020,ERS351214,,CGTACTAG,TAGATCGC,,qPCR only,CGTACTAGTAGATCGC,,,,,,,0,0,8381739,0,8215020,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351214,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706391,,mES_ai2_s2_cell2,mES_ai2_s2_cell2,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,2, diff --git a/t/data/samplesheet/6946_extended.csv b/t/data/samplesheet/6946_extended.csv index 563f3870..bfd0b845 100644 --- a/t/data/samplesheet/6946_extended.csv +++ b/t/data/samplesheet/6946_extended.csv @@ -1,14 +1,14 @@ [Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Sample_ID,Sample_Name,GenomeFolder,Index,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -3789278,Salmonella pullorum,,ATCACGTT,,Standard,ATCACGTT,,,,,,,0,0,3789299,0,3789278,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289832,,sp200shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,1, -3789279,Bordetella Pertussis,,CGATGTTT,,Standard,CGATGTTT,,,,,,,0,0,3789299,0,3789279,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289833,,bp200shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,2, -3789280,Plasmodium Falciparum,,TTAGGCAT,,Standard,TTAGGCAT,,,,,,,0,0,3789299,0,3789280,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289834,,3D7200shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,3, -3789281,Homo sapiens,,TGACCACT,,Standard,TGACCACT,,,,,,,0,0,3789299,0,3789281,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289835,,human200shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,4, -3789282,Salmonella pullorum,,ACAGTGGT,,Standard,ACAGTGGT,,,,,,,0,0,3789299,0,3789282,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289836,,sp300shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,5, -3789283,Bordetella Pertussis,,GCCAATGT,,Standard,GCCAATGT,,,,,,,0,0,3789299,0,3789283,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289837,,bp300shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,6, -3789284,Plasmodium Falciparum,,CAGATCTG,,Standard,CAGATCTG,,,,,,,0,0,3789299,0,3789284,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289838,,3D7300shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,7, -3789285,Homo sapiens,,ACTTGATG,,Standard,ACTTGATG,,,,,,,0,0,3789299,0,3789285,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289839,,human300shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,8, -3789286,Salmonella pullorum,,GATCAGCG,,Standard,GATCAGCG,,,,,,,0,0,3789299,0,3789286,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289840,,sp400shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,9, -3789287,Bordetella Pertussis,,TAGCTTGT,,Standard,TAGCTTGT,,,,,,,0,0,3789299,0,3789287,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289841,,bp400shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,10, -3789288,Plasmodium Falciparum,,GGCTACAG,,Standard,GGCTACAG,,,,,,,0,0,3789299,0,3789288,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289842,,3D7400shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,11, -3789289,Homo sapiens,,CTTGTACT,,Standard,CTTGTACT,,,,,,,0,0,3789299,0,3789289,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289843,,human400shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,0,0,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,0,hifi test,12, +3789278,Salmonella pullorum,,ATCACGTT,,Standard,ATCACGTT,,,,,,,0,0,3789299,0,3789278,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289832,,sp200shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,1, +3789279,Bordetella Pertussis,,CGATGTTT,,Standard,CGATGTTT,,,,,,,0,0,3789299,0,3789279,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289833,,bp200shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,2, +3789280,Plasmodium Falciparum,,TTAGGCAT,,Standard,TTAGGCAT,,,,,,,0,0,3789299,0,3789280,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289834,,3D7200shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,3, +3789281,Homo sapiens,,TGACCACT,,Standard,TGACCACT,,,,,,,0,0,3789299,0,3789281,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,1,,genomic DNA,,1289835,,human200shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,4, +3789282,Salmonella pullorum,,ACAGTGGT,,Standard,ACAGTGGT,,,,,,,0,0,3789299,0,3789282,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289836,,sp300shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,5, +3789283,Bordetella Pertussis,,GCCAATGT,,Standard,GCCAATGT,,,,,,,0,0,3789299,0,3789283,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289837,,bp300shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,6, +3789284,Plasmodium Falciparum,,CAGATCTG,,Standard,CAGATCTG,,,,,,,0,0,3789299,0,3789284,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289838,,3D7300shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,7, +3789285,Homo sapiens,,ACTTGATG,,Standard,ACTTGATG,,,,,,,0,0,3789299,0,3789285,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289839,,human300shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,8, +3789286,Salmonella pullorum,,GATCAGCG,,Standard,GATCAGCG,,,,,,,0,0,3789299,0,3789286,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289840,,sp400shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,9, +3789287,Bordetella Pertussis,,TAGCTTGT,,Standard,TAGCTTGT,,,,,,,0,0,3789299,0,3789287,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289841,,bp400shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,10, +3789288,Plasmodium Falciparum,,GGCTACAG,,Standard,GGCTACAG,,,,,,,0,0,3789299,0,3789288,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289842,,3D7400shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,11, +3789289,Homo sapiens,,CTTGTACT,,Standard,CTTGTACT,,,,,,,0,0,3789299,0,3789289,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289843,,human400shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,12, From 8186e2b4d469ff2a6c01791ae54b103d55d5239f Mon Sep 17 00:00:00 2001 From: mgcam Date: Tue, 10 Oct 2023 09:55:47 +0100 Subject: [PATCH 06/35] Capture current behaviour of the genome_reference method (#760) * Improved and extended basic tests for tag zero * Extended tests for study and sample properties --- MANIFEST | 1 + t/40-st-lims.t | 153 ++++++++++++++++------- t/data/samplesheet/samplesheet_47539.csv | 82 ++++++++++++ 3 files changed, 191 insertions(+), 45 deletions(-) create mode 100644 t/data/samplesheet/samplesheet_47539.csv diff --git a/MANIFEST b/MANIFEST index f6ae9ff0..b105dd9f 100644 --- a/MANIFEST +++ b/MANIFEST @@ -756,6 +756,7 @@ t/data/samplesheet/miseq_default_dual_index.csv t/data/samplesheet/miseq_extended.csv t/data/samplesheet/multilane.csv t/data/samplesheet/novaseq_multirun.csv +t/data/samplesheet/samplesheet_47539.csv t/data/st_api_lims_new/st/assets/3033734.xml t/data/st_api_lims_new/st/assets/3111688.xml t/data/st_api_lims_new/st/batches/12141.xml diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 9bba0b2c..cdc0a816 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -190,52 +190,62 @@ subtest 'Run-level object via samplesheet driver' => sub { is ($plexes[95]->sample_name, 'LIA_96', 'sample_name of the last plex'); }; -subtest 'Lane-level object via samplesheet driver' => sub { - plan tests => 14; +subtest 'Lane-level and tag zero objects via samplesheet driver' => sub { + plan tests => 20; my $path = 't/data/samplesheet/miseq_default.csv'; - lives_ok {st::api::lims->new(id_run => 10262, position =>2, path => $path, driver_type => 'samplesheet')} - 'no error instantiation an object for a non-existing lane'; - throws_ok {st::api::lims->new(id_run => 10262, position =>2, path => $path, driver_type => 'samplesheet')->library_id} - qr/Position 2 not defined in/, 'error invoking a driver method on an object for a non-existing lane'; - lives_ok {st::api::lims->new(id_run => 10262, position =>2, driver_type => 'samplesheet')} - 'no error instantiation an object without path'; - - my $ss=st::api::lims->new(id_run => 10262, position =>1, tag_index => 0, path => $path); - is (scalar $ss->children, 96, '96 children returned for tag zero'); - is ($ss->is_pool, 1, 'tag zero is a pool'); - is ($ss->library_id, undef, 'tag_zero library_id undefined'); - is ($ss->default_tag_sequence, undef, 'default tag sequence undefined'); - is ($ss->tag_sequence, undef, 'tag sequence undefined'); - is ($ss->purpose, undef, 'purpose'); + + my $l; + lives_ok { $l = st::api::lims->new( + id_run => 10262, position => 2, path => $path) + } 'no error instantiation an object for a non-existing lane'; + throws_ok { $l->library_id } + qr/Position 2 not defined in/, + 'error invoking a driver method on an object for a non-existing lane'; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $path; - $ss=st::api::lims->new(id_run => 10262, position =>1); - is ($ss->path, $path, 'samplesheet path captured from NPG_CACHED_SAMPLESHEET_FILE') or diag explain $ss; - is ($ss->position, 1, 'correct position'); - is ($ss->is_pool, 1, 'lane is a pool'); - is ($ss->library_id, undef, 'pool lane library_id undefined'); - is (scalar $ss->children, 96, '96 plexes returned'); + + my $lane = st::api::lims->new(id_run => 10262, position => 1); + is ($lane->tag_index, undef, 'tag index is undefined for a lane'); + my $tag_zero = st::api::lims->new(id_run => 10262, position => 1, tag_index => 0); + is ($tag_zero->tag_index, 0, 'tag index is zero for tag zero'); + for my $ss (($lane, $tag_zero)) { + is ($ss->path, $path, + 'samplesheet path captured from NPG_CACHED_SAMPLESHEET_FILE') + or diag explain $ss; + is ($ss->position, 1, 'correct position'); + is ($ss->is_pool, 1, 'entity is a pool'); + is (scalar $ss->children, 96, '96 plexes returned'); + is ($ss->library_id, undef, 'library_id undefined'); + is ($ss->sample_name, undef, 'sample name is undefined'); + is ($ss->default_tag_sequence, undef, 'default tag sequence undefined'); + is ($ss->tag_sequence, undef, 'tag sequence undefined'); + } }; -subtest 'Plex-level object via samplesheet driver' => sub { +subtest 'Plex-level objects via samplesheet driver' => sub { plan tests => 10; my $path = 't/data/samplesheet/miseq_default.csv'; - lives_ok {st::api::lims->new(id_run => 10262, position =>1, tag_index=>999,path => $path, driver_type => 'samplesheet')} - 'no error instantiation an object for a non-existing tag_index'; - throws_ok {st::api::lims->new(id_run => 10262, position =>1, tag_index => 999, path => $path, driver_type => 'samplesheet')->children} - qr/Tag index 999 not defined in/, 'error invoking a driver method on an object for a non-existing tag_index'; - - my $ss=st::api::lims->new(id_run => 10262, position =>1, tag_index => 3, path => $path, driver_type => 'samplesheet'); - is ($ss->position, 1, 'correct position'); - is ($ss->tag_index, 3, 'correct tag_index'); - is ($ss->is_pool, 0, 'plex is not a pool'); - is ($ss->default_tag_sequence, 'TTAGGCAT', 'correct default tag sequence'); - is ($ss->tag_sequence, $ss->default_tag_sequence, 'tag sequence is the same as default tag sequence'); - is ($ss->library_id, 7583413, 'library id is correct'); - is ($ss->sample_name, 'LIA_3', 'sample name is correct'); - is (scalar $ss->children, 0, 'zero children returned'); + my $l; + lives_ok { $l = st::api::lims->new( + id_run => 10262, position => 1, tag_index => 999, path => $path + )} 'no error instantiation an object for a non-existing tag_index'; + throws_ok { $l->children() } + qr/Tag index 999 not defined in/, + 'error invoking a driver method on an object for a non-existing tag_index'; + + $l =st::api::lims->new( + id_run => 10262, position => 1, tag_index => 3, path => $path); + is ($l->position, 1, 'correct position'); + is ($l->tag_index, 3, 'correct tag_index'); + is ($l->is_pool, 0, 'plex is not a pool'); + is ($l->default_tag_sequence, 'TTAGGCAT', 'correct default tag sequence'); + is ($l->tag_sequence, $l->default_tag_sequence, + 'tag sequence is the same as default tag sequence'); + is ($l->library_id, 7583413, 'library id is correct'); + is ($l->sample_name, 'LIA_3', 'sample name is correct'); + is (scalar $l->children, 0, 'zero children returned'); }; subtest 'Samplesheet driver for a one-component composition' => sub { @@ -651,15 +661,16 @@ subtest 'Insert size' => sub { $insert_size = $lims->required_insert_size; is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size'); - is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size'); + is ($insert_size->{$id}->{q[to]}, 1000,'required TO insert size'); }; subtest 'Study and sample properties' => sub { - plan tests => 12; + plan tests => 47; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/4pool4libs_extended.csv'; + # A simple non-indexed lane. my $lims = st::api::lims->new(id_run => 9999, position => 1); is( $lims->study_title(), 'Haemonchus contortus Ivermectin Resistance', 'study title' ); @@ -669,9 +680,15 @@ subtest 'Study and sample properties' => sub { is( $lims->study_publishable_name(), 'ERP000430', 'study accession number returned as publishable name'); ok( !$lims->alignments_in_bam, 'no alignments'); + is( $lims->sample_reference_genome, 'Haemonchus_contortus (V1_21June13)', + 'sample reference genome'); + is( $lims->study_reference_genome, q[ ], 'study reference genome'); + is( $lims->reference_genome, 'Haemonchus_contortus (V1_21June13)', + 'reference genome'); + # Individual plex. $lims = st::api::lims->new(id_run => 9999, position => 7, tag_index=> 76); - ok($lims->alignments_in_bam, 'do alignments'); + ok( $lims->alignments_in_bam, 'do alignments'); like( $lims->study_title(), qr/Mouse model to quantify genotype-epigenotype variations /, 'study title'); @@ -682,12 +699,58 @@ subtest 'Study and sample properties' => sub { 'accession is returned as study publishable name'); is( $lims->sample_publishable_name(), 'ERS354534', 'sample publishable name returns accession'); - ok(!$lims->separate_y_chromosome_data, 'do not separate y chromosome data'); + ok( !$lims->separate_y_chromosome_data, 'do not separate y chromosome data'); + is( $lims->sample_reference_genome, undef, 'sample reference genome'); + is( $lims->study_reference_genome, 'Mus_musculus (GRCm38)', + 'study reference genome'); + is( $lims->reference_genome, 'Mus_musculus (GRCm38)', 'reference genome'); + + # Indexed lane and tag zero for the same lane. + for my $l ( + st::api::lims->new(id_run => 9999, position => 7), + st::api::lims->new(id_run => 9999, position => 7, tag_index => 0) + ) { + is( $l->study_name(), + 'Mouse model to quantify genotype-epigenotype variations_RNA', + 'study name'); + is( $l->sample_name, undef, 'sample name undefined'); + is( $l->sample_reference_genome, undef, 'sample reference genome'); + is( $l->study_reference_genome, 'Mus_musculus (GRCm38)', + 'study reference genome'); + is( $l->reference_genome, 'Mus_musculus (GRCm38)', 'reference genome'); + } - $lims = st::api::lims->new(id_run => 9999, position => 7); - is( $lims->study_name(), - 'Mouse model to quantify genotype-epigenotype variations_RNA', - 'study name'); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/samplesheet_47539.csv'; + + # Multiple sample references within a pool, the same study. + my $study_name = 'SeqOps Novaseq X Validation'; + my $ref = 'Homo_sapiens (GRCh38_15_plus_hs38d1) [minimap2]'; + for my $l ( + st::api::lims->new(id_run => 47539, position => 1), + st::api::lims->new(id_run => 47537, position => 1, tag_index => 0) + ) { + is( $l->study_name(), $study_name, 'study name'); + is( $l->sample_name, undef, 'sample name undefined'); + is( $l->sample_reference_genome, undef, 'sample reference genome undefined'); + is( $l->study_reference_genome, $ref, 'study reference genome'); + is( $l->reference_genome, $ref, 'reference genome - fallback to study'); + } + + my $sample_ref = 'Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla)'; + $lims = st::api::lims->new(id_run => 47537, position => 1, tag_index => 1); + is( $lims->study_name(), $study_name, 'study name'); + is( $lims->sample_name, 'RefStds_PCR8021331', 'sample name'); + is( $lims->sample_reference_genome, $sample_ref, 'sample reference genome'); + is( $lims->study_reference_genome, $ref, 'study reference genome'); + is( $lims->reference_genome, $sample_ref, 'reference genome as for the sample'); + + $lims = st::api::lims->new(id_run => 47537, position => 4, tag_index => 2); + is( $lims->study_name(),$study_name, 'study name'); + is( $lims->sample_name, 'RefStds_PCR-free8023829', 'sample name'); + is( $lims->sample_reference_genome, undef, 'sample reference genome undefined'); + is( $lims->study_reference_genome, $ref, 'study reference genome'); + is( $lims->reference_genome, $ref, 'reference genome - fall back to study'); }; subtest 'Bait name' => sub { diff --git a/t/data/samplesheet/samplesheet_47539.csv b/t/data/samplesheet/samplesheet_47539.csv new file mode 100644 index 00000000..69a65874 --- /dev/null +++ b/t/data/samplesheet/samplesheet_47539.csv @@ -0,0 +1,82 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,28479597,RefStds_PCR8021331,,GTTCAAAG,TGCATAAA,,Standard,GTTCAAAG,TGCATAAA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159160,,RefStds_PCR8021331,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +1,28479657,RefStds_PCR8021365,,GTCGCGAC,ACACCTTA,,Standard,GTCGCGAC,ACACCTTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,4159165,,RefStds_PCR8021365,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +1,28479586,RefStds_PCR8021381,,CCAGGTCG,TCACTGGA,,Standard,CCAGGTCG,TCACTGGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,4159167,,RefStds_PCR8021381,,Escherichia_coli (K12),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +1,28479610,RefStds_PCR8021397,,AAGGCCGC,TTTAGACA,,Standard,AAGGCCGC,TTTAGACA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,4159169,,RefStds_PCR8021397,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +1,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +2,28479597,RefStds_PCR8021331,,GTTCAAAG,TGCATAAA,,Standard,GTTCAAAG,TGCATAAA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159160,,RefStds_PCR8021331,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +2,28479609,RefStds_PCR8021333,,TTAACTTA,GTCATCCT,,Standard,TTAACTTA,GTCATCCT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159161,,RefStds_PCR8021333,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +2,28479621,RefStds_PCR8021347,,GCCTAGGG,AGTTGGAG,,Standard,GCCTAGGG,AGTTGGAG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159162,,RefStds_PCR8021347,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +2,28479633,RefStds_PCR8021349,,CGAGGGTT,TGCGCTCA,,Standard,CGAGGGTT,TGCGCTCA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159163,,RefStds_PCR8021349,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +2,28479645,RefStds_PCR8021363,,GAGCGAAC,TGGTAAAG,,Standard,GAGCGAAC,TGGTAAAG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159164,,RefStds_PCR8021363,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +2,28479657,RefStds_PCR8021365,,GTCGCGAC,ACACCTTA,,Standard,GTCGCGAC,ACACCTTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,4159165,,RefStds_PCR8021365,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +2,28479574,RefStds_PCR8021379,,GTCTTGCC,TCTGCCCT,,Standard,GTCTTGCC,TCTGCCCT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159166,,RefStds_PCR8021379,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +2,28479586,RefStds_PCR8021381,,CCAGGTCG,TCACTGGA,,Standard,CCAGGTCG,TCACTGGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,4159167,,RefStds_PCR8021381,,Escherichia_coli (K12),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +2,28479598,RefStds_PCR8021395,,CGTGTGGA,ACCGATTA,,Standard,CGTGTGGA,ACCGATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159168,,RefStds_PCR8021395,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +2,28479610,RefStds_PCR8021397,,AAGGCCGC,TTTAGACA,,Standard,AAGGCCGC,TTTAGACA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,4159169,,RefStds_PCR8021397,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +2,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +3,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +3,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +3,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +3,66843860,RefStds_PCR-free8023845,,CCGTGAAG,CAGTGGAT,,HiSeqX PCR free,CCGTGAAG,CAGTGGAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159410,,RefStds_PCR-free8023845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +3,66843814,RefStds_PCR-free8023857,,ATATGGAT,CTGTATTA,,HiSeqX PCR free,ATATGGAT,CTGTATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720937,,RefStds_PCR-free8023857,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +3,66843862,RefStds_PCR-free8023861,,ATGGCATG,AAGGTACC,,HiSeqX PCR free,ATGGCATG,AAGGTACC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159412,,RefStds_PCR-free8023861,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +3,66843816,RefStds_PCR-free8023873,,TGCGGCGT,CCTCGGTA,,HiSeqX PCR free,TGCGGCGT,CCTCGGTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720943,,RefStds_PCR-free8023873,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +3,66843864,RefStds_PCR-free8023877,,CGGAACTG,CACTACGA,,HiSeqX PCR free,CGGAACTG,CACTACGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,36329,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Malaria,,,,,4159414,,RefStds_PCR-free8023877,,Plasmodium_falciparum (3D7_Jan16v3),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +3,66843818,RefStds_PCR-free8023889,,CAATTAAC,CGAGATAT,,HiSeqX PCR free,CAATTAAC,CGAGATAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720949,,RefStds_PCR-free8023889,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +3,66843866,RefStds_PCR-free8023893,,TGCGAGAC,CATTGTTG,,HiSeqX PCR free,TGCGAGAC,CATTGTTG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,8720952,,RefStds_PCR-free8023893,,Escherichia_coli (K12_DH10B),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +3,66843820,RefStds_PCR-free8023905,,TATCGCAC,CTTAGTGT,,HiSeqX PCR free,TATCGCAC,CTTAGTGT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,8720956,,RefStds_PCR-free8023905,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,11, +3,66843868,RefStds_PCR-free8023909,,TACTCATA,CCTGTGGC,,HiSeqX PCR free,TACTCATA,CCTGTGGC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,8720960,,RefStds_PCR-free8023909,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,12, +3,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +4,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +4,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +4,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +5,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +5,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +5,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +5,66843860,RefStds_PCR-free8023845,,CCGTGAAG,CAGTGGAT,,HiSeqX PCR free,CCGTGAAG,CAGTGGAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159410,,RefStds_PCR-free8023845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +5,66843814,RefStds_PCR-free8023857,,ATATGGAT,CTGTATTA,,HiSeqX PCR free,ATATGGAT,CTGTATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720937,,RefStds_PCR-free8023857,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +5,66843862,RefStds_PCR-free8023861,,ATGGCATG,AAGGTACC,,HiSeqX PCR free,ATGGCATG,AAGGTACC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159412,,RefStds_PCR-free8023861,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +5,66843816,RefStds_PCR-free8023873,,TGCGGCGT,CCTCGGTA,,HiSeqX PCR free,TGCGGCGT,CCTCGGTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720943,,RefStds_PCR-free8023873,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +5,66843864,RefStds_PCR-free8023877,,CGGAACTG,CACTACGA,,HiSeqX PCR free,CGGAACTG,CACTACGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,36329,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Malaria,,,,,4159414,,RefStds_PCR-free8023877,,Plasmodium_falciparum (3D7_Jan16v3),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +5,66843818,RefStds_PCR-free8023889,,CAATTAAC,CGAGATAT,,HiSeqX PCR free,CAATTAAC,CGAGATAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720949,,RefStds_PCR-free8023889,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +5,66843866,RefStds_PCR-free8023893,,TGCGAGAC,CATTGTTG,,HiSeqX PCR free,TGCGAGAC,CATTGTTG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,8720952,,RefStds_PCR-free8023893,,Escherichia_coli (K12_DH10B),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +5,66843820,RefStds_PCR-free8023905,,TATCGCAC,CTTAGTGT,,HiSeqX PCR free,TATCGCAC,CTTAGTGT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,8720956,,RefStds_PCR-free8023905,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,11, +5,66843868,RefStds_PCR-free8023909,,TACTCATA,CCTGTGGC,,HiSeqX PCR free,TACTCATA,CCTGTGGC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,8720960,,RefStds_PCR-free8023909,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,12, +5,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +6,66843810,RefStds_PCR-free8023825,,AGTTCAGG,CCAACAGA,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720924,,RefStds_PCR-free8023825,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,1, +6,66843858,RefStds_PCR-free8023829,,CCAAGTCT,AAGGATGA,,HiSeqX PCR free,CCAAGTCT,AAGGATGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,,,,,,8720927,,RefStds_PCR-free8023829,,,,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,2, +6,66843812,RefStds_PCR-free8023841,,ACTAAGAT,AACCGCGG,,HiSeqX PCR free,ACTAAGAT,AACCGCGG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720931,,RefStds_PCR-free8023841,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,3, +6,66843860,RefStds_PCR-free8023845,,CCGTGAAG,CAGTGGAT,,HiSeqX PCR free,CCGTGAAG,CAGTGGAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159410,,RefStds_PCR-free8023845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,4, +6,66843814,RefStds_PCR-free8023857,,ATATGGAT,CTGTATTA,,HiSeqX PCR free,ATATGGAT,CTGTATTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720937,,RefStds_PCR-free8023857,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,5, +6,66843862,RefStds_PCR-free8023861,,ATGGCATG,AAGGTACC,,HiSeqX PCR free,ATGGCATG,AAGGTACC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,4159412,,RefStds_PCR-free8023861,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,6, +6,66843816,RefStds_PCR-free8023873,,TGCGGCGT,CCTCGGTA,,HiSeqX PCR free,TGCGGCGT,CCTCGGTA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720943,,RefStds_PCR-free8023873,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,7, +6,66843864,RefStds_PCR-free8023877,,CGGAACTG,CACTACGA,,HiSeqX PCR free,CGGAACTG,CACTACGA,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,36329,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Malaria,,,,,4159414,,RefStds_PCR-free8023877,,Plasmodium_falciparum (3D7_Jan16v3),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,8, +6,66843818,RefStds_PCR-free8023889,,CAATTAAC,CGAGATAT,,HiSeqX PCR free,CAATTAAC,CGAGATAT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Homo sapiens,,,,,8720949,,RefStds_PCR-free8023889,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,9, +6,66843866,RefStds_PCR-free8023893,,TGCGAGAC,CATTGTTG,,HiSeqX PCR free,TGCGAGAC,CATTGTTG,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,511145,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Escherichia coli,,,,,8720952,,RefStds_PCR-free8023893,,Escherichia_coli (K12_DH10B),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,10, +6,66843820,RefStds_PCR-free8023905,,TATCGCAC,CTTAGTGT,,HiSeqX PCR free,TATCGCAC,CTTAGTGT,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,272563,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Clostridioides difficile,,,,,8720956,,RefStds_PCR-free8023905,,Clostridium_difficile (Strain_630),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,11, +6,66843868,RefStds_PCR-free8023909,,TACTCATA,CCTGTGGC,,HiSeqX PCR free,TACTCATA,CCTGTGGC,user1@some.com user2@some.com,,user2@some.com,user1@some.com,,0,0,,,,,257313,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:450 to:450,,,Bordetella pertussis,,,,,8720960,,RefStds_PCR-free8023909,,Bordetella_pertussis (Tohama_I),,888,,1,0,0,Samples are being submitted to test the new NovaSeq X,7309,SeqOps Novaseq X Validation,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,,SeqOps Novaseq X Validation,12, +6,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, +7,65828605,EGAN00004178291,,CCGTTAGT,ATCACGAT,,RNA Poly A Globin,CCGTTAGT,ATCACGAT,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178291,,Homo Sapiens,,,,,8511812,,pops212973524,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,1, +7,65828617,EGAN00004178293,,TCGACTCG,TGATCAAA,,RNA Poly A Globin,TCGACTCG,TGATCAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178293,,Homo Sapiens,,,,,8511814,,pops212973526,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,2, +7,65828629,EGAN00004178294,,CGTAAAGA,CGACTTCC,,RNA Poly A Globin,CGTAAAGA,CGACTTCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178294,,Homo Sapiens,,,,,8511815,,pops212973527,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,3, +7,65828641,EGAN00004178295,,CGTCGTCG,CTCAGAAA,,RNA Poly A Globin,CGTCGTCG,CTCAGAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178295,,Homo Sapiens,,,,,8511816,,pops212973528,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,4, +7,65828653,EGAN00004178297,,TTCTCTTT,TCAGCCTG,,RNA Poly A Globin,TTCTCTTT,TCAGCCTG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178297,,Homo Sapiens,,,,,8511817,,pops212973529,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,5, +7,65828665,EGAN00004178299,,TCTCATAT,TTTGCACC,,RNA Poly A Globin,TCTCATAT,TTTGCACC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178299,,Homo Sapiens,,,,,8511819,,pops212973531,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,6, +7,65828677,EGAN00004178300,,TCGGGCTG,CGATCTGG,,RNA Poly A Globin,TCGGGCTG,CGATCTGG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178300,,Homo Sapiens,,,,,8511820,,pops212973532,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,7, +7,65828689,EGAN00004178301,,GGAACGAT,GGCGTCCC,,RNA Poly A Globin,GGAACGAT,GGCGTCCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178301,,Homo Sapiens,,,,,8511821,,pops212973533,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,8, +7,65828606,EGAN00004178302,,TGTTACAG,GAGCGCGC,,RNA Poly A Globin,TGTTACAG,GAGCGCGC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178302,,Homo Sapiens,,,,,8511823,,pops212973535,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,9, +7,65828618,EGAN00004178304,,TCCACAAA,TGGTGCAC,,RNA Poly A Globin,TCCACAAA,TGGTGCAC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178304,,Homo Sapiens,,,,,8511824,,pops212973536,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,10, +7,65828630,EGAN00004178305,,CGCCTTGA,TGGTGACT,,RNA Poly A Globin,CGCCTTGA,TGGTGACT,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178305,,Homo Sapiens,,,,,8511825,,pops212973537,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,11, +8,65828605,EGAN00004178291,,CCGTTAGT,ATCACGAT,,RNA Poly A Globin,CCGTTAGT,ATCACGAT,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178291,,Homo Sapiens,,,,,8511812,,pops212973524,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,1, +8,65828617,EGAN00004178293,,TCGACTCG,TGATCAAA,,RNA Poly A Globin,TCGACTCG,TGATCAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178293,,Homo Sapiens,,,,,8511814,,pops212973526,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,2, +8,65828629,EGAN00004178294,,CGTAAAGA,CGACTTCC,,RNA Poly A Globin,CGTAAAGA,CGACTTCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178294,,Homo Sapiens,,,,,8511815,,pops212973527,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,3, +8,65828641,EGAN00004178295,,CGTCGTCG,CTCAGAAA,,RNA Poly A Globin,CGTCGTCG,CTCAGAAA,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178295,,Homo Sapiens,,,,,8511816,,pops212973528,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,4, +8,65828653,EGAN00004178297,,TTCTCTTT,TCAGCCTG,,RNA Poly A Globin,TTCTCTTT,TCAGCCTG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178297,,Homo Sapiens,,,,,8511817,,pops212973529,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,5, +8,65828665,EGAN00004178299,,TCTCATAT,TTTGCACC,,RNA Poly A Globin,TCTCATAT,TTTGCACC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178299,,Homo Sapiens,,,,,8511819,,pops212973531,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,6, +8,65828677,EGAN00004178300,,TCGGGCTG,CGATCTGG,,RNA Poly A Globin,TCGGGCTG,CGATCTGG,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178300,,Homo Sapiens,,,,,8511820,,pops212973532,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,7, +8,65828689,EGAN00004178301,,GGAACGAT,GGCGTCCC,,RNA Poly A Globin,GGAACGAT,GGCGTCCC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178301,,Homo Sapiens,,,,,8511821,,pops212973533,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,8, +8,65828606,EGAN00004178302,,TGTTACAG,GAGCGCGC,,RNA Poly A Globin,TGTTACAG,GAGCGCGC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178302,,Homo Sapiens,,,,,8511823,,pops212973535,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,9, +8,65828618,EGAN00004178304,,TCCACAAA,TGGTGCAC,,RNA Poly A Globin,TCCACAAA,TGGTGCAC,user3@some.com user5@some.com user4@some.com nf10@some.com,user3@some.com user4@some.com nf10@some.com,user3@some.com,user5@some.com,,0,0,,,,,9606,S0910,3780,SeqOps Novaseq X Validation,standard,,,from:100 to:300,EGAN00004178304,,Homo Sapiens,,,,,8511824,,pops212973536,,,,888,EGAS00001006379,1,0,0, There have been few previous studies,6947,I3636_HG_PoPs2_RNAseq,Homo_sapiens (GRCh38_15_plus_hs38d1 %2B ensembl_90_transcriptome) %5Bstar%5D,,Genetic Determinants,10, +8,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,,,PhiX UDI 20211019 %2312,,10847,,,,standard,,,,,,,,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls,,,,888, From 10bcd8fd1a20a5e4795ba2f62bd528b0d2ba8a40 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 12 Oct 2023 16:42:49 +0100 Subject: [PATCH 07/35] Deleted low-level LIMS XML API --- Build.PL | 1 - MANIFEST | 14 -- lib/npg/api/request.pm | 489 ----------------------------------------- lib/npg/api/util.pm | 203 ----------------- lib/st/api/base.pm | 321 --------------------------- lib/st/api/batch.pm | 89 -------- lib/st/api/project.pm | 105 --------- lib/st/api/sample.pm | 230 ------------------- lib/st/api/study.pm | 268 ---------------------- t/30-api-request.t | 149 ------------- t/30-api-util.t | 45 ---- t/40-st-base.t | 25 --- t/40-st-batch.t | 9 - t/40-st-project.t | 22 -- t/40-st-sample.t | 42 ---- t/40-st-study.t | 63 ------ 16 files changed, 2075 deletions(-) delete mode 100644 lib/npg/api/request.pm delete mode 100644 lib/npg/api/util.pm delete mode 100644 lib/st/api/base.pm delete mode 100644 lib/st/api/batch.pm delete mode 100644 lib/st/api/project.pm delete mode 100644 lib/st/api/sample.pm delete mode 100644 lib/st/api/study.pm delete mode 100644 t/30-api-request.t delete mode 100644 t/30-api-util.t delete mode 100644 t/40-st-base.t delete mode 100644 t/40-st-batch.t delete mode 100644 t/40-st-project.t delete mode 100644 t/40-st-sample.t delete mode 100644 t/40-st-study.t diff --git a/Build.PL b/Build.PL index f9da0065..b01e138b 100644 --- a/Build.PL +++ b/Build.PL @@ -121,7 +121,6 @@ my $builder = $class->new( 'base' => '2.12', 'Carp' => '1.04', 'CGI' => '3.52', - 'Class::Accessor' => '0.31', 'Class::Load' => 0, 'Class::Std' => '0.0.8', 'ClearPress' => '>= 473.3.3', diff --git a/MANIFEST b/MANIFEST index b105dd9f..5dad2d69 100644 --- a/MANIFEST +++ b/MANIFEST @@ -122,8 +122,6 @@ INSTALL lib/Monitor/RunFolder.pm lib/Monitor/RunFolder/Staging.pm lib/Monitor/Staging.pm -lib/npg/api/request.pm -lib/npg/api/util.pm lib/npg/authentication/sanger_ldap.pm lib/npg/authentication/sanger_sso.pm lib/npg/controller.pm @@ -274,17 +272,12 @@ lib/npg_tracking/util/db_connect.pm lib/npg_tracking/util/messages.pm lib/npg_tracking/util/pipeline_config.pm lib/npg_tracking/util/types.pm -lib/st/api/base.pm -lib/st/api/batch.pm lib/st/api/lims.pm lib/st/api/lims/samplesheet.pm lib/st/api/lims/ml_warehouse/driver.pm lib/st/api/lims/ml_warehouse.pm lib/st/api/lims/ml_warehouse_auto.pm lib/st/api/lims/ml_warehouse_fc_cache.pm -lib/st/api/project.pm -lib/st/api/sample.pm -lib/st/api/study.pm MANIFEST This list of files README README.md @@ -399,21 +392,14 @@ t/20-view-user2usergroup.t t/20-view-usergroup.t t/20-view.t t/25-template-actions.t -t/30-api-request.t -t/30-api-util.t t/34-monitor-runfolder-staging.t t/34-monitor-runfolder.t t/34-monitor-staging.t t/35-monitor_one_runfolder.t -t/40-st-base.t -t/40-st-batch.t t/40-st-lims-mlwarehouse.t t/40-st-lims-ml_warehouse-drivers.t t/40-st-lims-samplesheet.t t/40-st-lims.t -t/40-st-project.t -t/40-st-sample.t -t/40-st-study.t t/47-samplesheet.t t/47-npg_samplesheet_novaseq_xseries.t t/47-npg_samplesheet_auto.t diff --git a/lib/npg/api/request.pm b/lib/npg/api/request.pm deleted file mode 100644 index 68cb88aa..00000000 --- a/lib/npg/api/request.pm +++ /dev/null @@ -1,489 +0,0 @@ -############# -# Created By: Marina Gourtovaia -# Created On: 11 June 2010 - -package npg::api::request; - -use Carp; -use English qw( -no_match_vars ); -use Moose; -use Moose::Util::TypeConstraints; -use MooseX::StrictConstructor; -use MooseX::ClassAttribute; -use LWP::UserAgent; -use HTTP::Request::Common; -use File::Basename; -use File::Path; -use File::Spec::Functions qw(catfile); -use Readonly; - -our $VERSION = '0'; - -## no critic (RequirePodAtEnd RequireCheckingReturnValueOfEval) - -=head1 NAME - -npg::api::request - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -Performs requests to web services on behalf on NPG software. -Retrieves requested contents either from a specified URI or from a cache. -When retrieving the contents from URI can, optionally, save the resource -to cache. - -The location of the cache is stored in an environment variable - -=head1 SUBROUTINES/METHODS - -=cut - -Readonly::Scalar our $DEFAULT_VAR_NAME => q[NPG_WEBSERVICE_CACHE_DIR]; -Readonly::Scalar our $SAVE2CACHE_VAR_NAME => q[SAVE2NPG_WEBSERVICE_CACHE]; - -Readonly::Scalar our $MAX_RETRIES => 10; -Readonly::Scalar our $RETRY_DELAY => 10; -Readonly::Scalar our $LWP_TIMEOUT => 60; -Readonly::Scalar our $LWP_TIMEOUT_POST => $LWP_TIMEOUT * 2; -Readonly::Scalar our $DEFAULT_METHOD => q[GET]; -Readonly::Scalar our $DEFAULT_CONTENT_TYPE => q[text/xml]; - - -subtype 'NPG_API_Request_PositiveInt' - => as Int - => where { $_ > 0 }; - - -=head2 cache_dir_var_name - -Name of the environmental variable that defines the location -of the cache. Class attribute. - -=cut -class_has 'cache_dir_var_name'=> (isa => 'Str', - is => 'ro', - required => 0, - default => $DEFAULT_VAR_NAME, - ); - -=head2 cache_dir_var_name - -Name of the environmental variable that defines whether -the retrieved files have to be saved to cache. Class attribute. - -=cut -class_has 'save2cache_dir_var_name'=> (isa => 'Str', - is => 'ro', - required => 0, - default => $SAVE2CACHE_VAR_NAME, - ); - -=head2 max_retries - -Maximum number of attempts to retrieve a requested resource. - -=cut -has 'max_retries'=> (isa => 'NPG_API_Request_PositiveInt', - is => 'ro', - required => 0, - default => $MAX_RETRIES, - ); - -=head2 retry_delay - -A delay (in seconds) between attempts. - -=cut -has 'retry_delay'=> (isa => 'NPG_API_Request_PositiveInt', - is => 'ro', - required => 0, - default => $RETRY_DELAY, - ); - -=head2 content_type - -Content type to accept - -=cut -has 'content_type'=> (isa => 'Maybe[Str]', - is => 'ro', - required => 0, - ); - -=head2 useragent - -Useragent for making an HTTP request. - -=cut -has 'useragent' => (isa => 'Object', - is => 'ro', - required => 0, - lazy_build => 1, - ); -sub _build_useragent { - my $self = shift; - - my $ua = LWP::UserAgent->new(); - $ua->agent(join q[/], __PACKAGE__, $VERSION); - $ua->timeout($LWP_TIMEOUT); - $ua->env_proxy(); - return $ua; -} - -=head2 login - -login for making a HTTP request - -=cut -has 'login' => (isa => 'Maybe[Str]', - is => 'ro', - required => 0, - ); - -=head2 password - -password to go with login above - -=cut -has 'password' =>(isa => 'Maybe[Str]', - is => 'ro', - required => 0, - ); - - -=head2 make - -Contacts a web service to perform a requested operation. -For GET requests optionally saves the content of a requested web resource -to a cache. If a global variable whose name is returned by -$self->cache_dir_var_name is set, for GET requests retrieves the -requested resource from a cache. - -=cut -sub make { - my ($self, $uri, $method, $args) = @_; - - if (!$uri) { - croak q[Uri is not defined]; - } - - if (!$method) { - $method = $DEFAULT_METHOD; - } - - my $cache = $ENV{$self->cache_dir_var_name} ? $ENV{$self->cache_dir_var_name} : q[]; - - my $content; - - if ($method ne $DEFAULT_METHOD) { - if ($cache) { - croak qq[$method requests cannot use cache: $uri]; - } - $content = $self->_from_web($uri, $method, $args); - } else { - my $path = q[]; - if ($cache) { - $self->_check_cache_dir($cache); - $path = $self->_create_path($uri); - if (!$path) { - croak qq[Empty path generated for $uri]; - } - } - - $content = ($cache && !$ENV{$self->save2cache_dir_var_name}) ? - $self->_from_cache($path, $uri) : - $self->_from_web($uri, $method, $args, $path); - if (!$content) { - croak qq[Empty document at $uri $path]; - } - } - - return $content; -} - - -sub _create_path { - my ( $self, $url ) = @_; - - my ($stpath) = $url =~ m{\Ahttps?://(?:(?:dev|sequencescape)\.)? - psd.* - \.sanger\.ac\.uk?(?::\d+)? - (/.*?)\z}xms; # sequencescape path - ##no critic(ProhibitComplexRegexes) - my ($npgpath) = $url =~ m{\Ahttps?:// - (?:npg|sfweb|sf2-farm-srv1) - (?:\.(?:dev|internal))? - \.sanger\.ac\.uk?(?::\d+)? - \/perl\/npg\/ - (.*?)\z}xms; # npg path - ##use critic - my ($extpath) = $url =~ m{\Ahttps?://.*?/(.*?)\z}xms; # other source path - - my $path = $stpath || $npgpath || $extpath; - $path =~ s/[ ]/_/gxms; # swap spaces for underscores - ($path) = $path =~ m{([/[:lower:][:digit:]_.]+)}xms; # get rid of horrible characters - $path =~ s{\A/}{}xms; # stop double // before path - - if ($npgpath) { - $path = catfile(q{npg}, $path); - } elsif ($stpath) { - $path = catfile(q{st}, $path); - } elsif ($extpath) { - $path = catfile(q{ext}, $path); - } - - if ($path) { - $path = catfile($ENV{$self->cache_dir_var_name}, $path); - } - return $path; -} - - -sub _check_cache_dir { - my ($self, $cache) = @_; - - if (!-e $cache) { - croak qq[Cache directory $cache does not exist]; - } - if (!-d $cache) { - croak qq[$cache (a proposed cache directory) is not a directory]; - } - if ($ENV{$self->save2cache_dir_var_name}) { - if (!-w $cache) { - croak qq[Cache directory $cache is not writable]; - } - } else { - if (!-r $cache) { - croak qq[Cache directory $cache is not readable]; - } - } - return 1; -} - -sub _from_cache { - my ($self, $path, $uri) = @_; - - $path .= $self->_extension($self->content_type); - if (!-e $path) { - croak qq[$path for $uri is not in the cache]; - } - - local $RS = undef; - open my $fh, q[<], $path or croak qq[Error when opening $path for reading: $ERRNO]; - if (!defined $fh) { croak qq[Undefined filehandle returned for $path]; } - my $content = defined $fh ? <$fh> : croak qq[Failed to read from an open $path: $ERRNO]; - close $fh or croak qq[Failed to close a filehandle for $path: $ERRNO]; - - return $content; -} - -sub _from_web { - my ($self, $uri, $method, $args, $path) = @_; - - if ($path && $ENV{$self->save2cache_dir_var_name} && $ENV{$self->cache_dir_var_name}) { - my $content; - eval { - $content = $self->_from_cache($path, $uri); - }; - if ($content) { - return $content; - } - } - - my $req; - if ($method eq $DEFAULT_METHOD) { - $req = GET $uri, @{$args||[]}; - } else { - $req = POST $uri, @{$args||[]}; - $self->useragent()->timeout($LWP_TIMEOUT_POST); - } - if ($self->content_type) { - $req->header('Accept' => $self->content_type); - } - $self->_personalise_request($req); - if ($self->login) { - $req->authorization_basic($self->login, $self->password); - } - - my $response = $self->_retry(sub { - my $inner_response = $self->useragent()->request($req); - if(!$inner_response->is_success()) { - croak $inner_response->status_line(); - } - return $inner_response; - }, $uri); - - if(!$response->is_success()) { - croak qq[Web request to $uri failed: ] . $response->status_line(); - } - - my $content = $response->content(); - if($content =~ /An[ ]Error[ ]Occurred/smix) { - my ($errstr) = $content =~ m{

(Error.*?)

}smix; - croak $errstr; - } - - if (defined $self->content_type && $self->content_type eq $DEFAULT_CONTENT_TYPE && $content =~ /save2cache_dir_var_name}) { - my $content_type = $response->headers->header('Content-Type'); - if (!$content_type) { - $content_type = $self->content_type; - } - $self->_write2cache($path, $content, $content_type); - } - - return $content; -} - - -sub _write2cache { - my ($self, $path, $content, $content_type) = @_; - - $path .= $self->_extension($content_type); - - my ($name,$dir,$suffix) = fileparse($path); - if (-e $dir) { - if (!-d $dir) { - croak qq[$dir should be a directory]; - } - } else { - File::Path::make_path($dir); - } - - open my $fh, q[>], $path or croak qq[Error when opening $path for writing: $ERRNO]; - $fh or croak qq[Undefined filehandle returned for $path]; - print {$fh} $content or croak qq[Failed to write to open $path: $ERRNO]; - close $fh or croak qq[Failed to close a filehandle for $path: $ERRNO]; - return; -} - - -sub _retry { - my ($self, $cb, $uri) = @_; - - my $retry = 0; - my $result; - my $error; - - while($retry < $self->max_retries) { - $retry++; - eval { - $error = q[]; - $result = $cb->(); - } or do { - $error = $EVAL_ERROR; - }; - - if($result) { - last; - } - - if($retry == $self->max_retries) { - croak q[Failed ] . $self->max_retries . - qq[ attempts to request $uri. Giving up. Last error: $error]; - } - - sleep $self->retry_delay; - } - - return $result; -} - - -sub _extension { - my ($self, $content_type) = @_; - - my $extension = q[]; - if ($content_type) { - my @types = split /;/smx, $content_type; - @types = split /\//smx, $types[0]; - $extension = q[.] . $types[-1]; - } - return $extension; -} - - -sub _personalise_request { - my ($self, $req) = @_; - - my $user = q[]; - eval {$user = getlogin;}; - if ($user) { - $req->header('X-username' => $user); - } - return; -} - - -1; - -__END__ - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item Moose - -=item Moose::Util::TypeConstraints - -=item MooseX::StrictConstructor - -=item Readonly - -=item Carp - -=item English - -=item LWP::UserAgent - -=item HTTP::Request::Common - -=item File::Basename - -=item File::Path - -=item File::Spec::Functions - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Marina Gourtovaia - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2010,2020 Genome Research Ltd. by Marina Gourtovaia - -This file is part of NPG. - -NPG is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut diff --git a/lib/npg/api/util.pm b/lib/npg/api/util.pm deleted file mode 100644 index 78e5f34a..00000000 --- a/lib/npg/api/util.pm +++ /dev/null @@ -1,203 +0,0 @@ -######### -# Author: rmp -# Created: 2007-03-28 -# -# -# This module is now DEPRACATED. Do not use. Use npg::api::request directly instead. -# js10 5th June 2014 -# -package npg::api::util; - -use strict; -use warnings; -use base qw(Class::Accessor); -use Carp; -use XML::LibXML; -use Readonly; - -use npg::api::request; - -our $VERSION = '0'; - -Readonly::Scalar our $LIVE_BASE_URI => 'http://sfweb.internal.sanger.ac.uk:9000/perl/npg'; -Readonly::Scalar our $DEV_BASE_URI => 'http://sf2-farm-srv2.internal.sanger.ac.uk:9010/perl/npg'; - -Readonly::Scalar our $MAX_RETRIES => 3; -Readonly::Scalar our $RETRY_DELAY => 5; - -sub new { - my ($class, $ref) = @_; - $ref ||= {}; - bless $ref, $class; - return $ref; -} - -sub parser { - my $self = shift; - $self->{'parser'} ||= XML::LibXML->new(); - return $self->{'parser'}; -} - -sub max_retries { - my ($self, $v) = @_; - if(defined $v) { - $self->{max_retries} = $v; - } - return $self->{max_retries} || $MAX_RETRIES; -} - -sub retry_delay { - my ($self, $v) = @_; - if(defined $v) { - $self->{retry_delay} = $v; - } - return $self->{retry_delay} || $RETRY_DELAY; -} - -sub useragent { - my $self = shift; - - if(!$self->{'useragent'}) { - my $ua = LWP::UserAgent->new(); - $ua->agent("npg::api::util/$VERSION "); - $ua->env_proxy(); - $self->{'useragent'} = $ua; - } - return $self->{'useragent'}; -} - -sub request { - my ($self, $content_type) = @_; - my $h = {}; - $h->{max_retries} = $self->max_retries; - $h->{retry_delay} = $self->retry_delay; - if ($content_type) { - $h->{content_type} = $content_type; - } - if ($self->{useragent}) { - $h->{useragent} = $self->{useragent}; - } - return npg::api::request->new($h); -} - -sub base_uri { - my $self = shift; - if ($self->{base_uri}) { - return $self->{base_uri}; - } - my $dev = $ENV{dev} || q{live}; - - $self->{base_uri} = $dev eq q{dev} ? $DEV_BASE_URI : $LIVE_BASE_URI; - return $self->{base_uri}; -} - -sub get { - my ($self, $uri, $args) = @_; - return $self->request('text/xml')->make($uri, q[GET], $args); -} - -sub post { - my ($self, $uri, $args) = @_; - return $self->request('text/xml')->make($uri, q[POST], $args); -} - -1; -__END__ - -=head1 NAME - -npg::api::util - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -=head1 SUBROUTINES/METHODS - -=head2 new - Constructor - -May take optional base_uri, useragent and parser attributes, see respective methods below. - - my $oUtil = npg::api::util->new(); - my $oUtil = npg::api::util->new({ - 'base_uri' => 'http://npg.sanger.ac.uk/perl/npg', - 'useragent' => LWP::UserAgent->new(), - 'parser' => XML::LibXML->new(); - }); - -=head2 parser - an instance of XML parser - -=head2 useragent - -=head2 max_retries - -=head2 retry_delay - -=head2 request - an instance of npg::api::request object - -=head2 base_uri - base URI for this resource set - - my $sURI = $oDerivedObject->base_uri(); - -=head2 get - HTTP GET with additional Accept: text/XML header - -=head2 post - HTTP POST with additional Accept: text/XML header - -=head2 post_non_xml - HTTP POST without Accept:text/XML header - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item base - -=item strict - -=item warnings - -=item Readonly - -=item Class::Accessor - -=item Carp - -=item XML::LibXML - -=item npg::api::request - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Roger Pettett, Ermp@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2010 GRL, by Roger Pettett - -This file is part of NPG. - -NPG is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut diff --git a/lib/st/api/base.pm b/lib/st/api/base.pm deleted file mode 100644 index c7b8a9c1..00000000 --- a/lib/st/api/base.pm +++ /dev/null @@ -1,321 +0,0 @@ -######### -# Author: rmp -# Created: 2007-03-28 -# -package st::api::base; - -use base qw(Class::Accessor); -use strict; -use warnings; -use Carp; - -use npg::api::util; - -our $VERSION = '0'; - -sub live_url { return q{http://sequencescape.psd.sanger.ac.uk}; } -sub dev_url { return q{http://dev.psd.sanger.ac.uk:6610}; } - -sub lims_url { - my $live = q{live}; - my $domain = $ENV{'dev'} || $live; - return $domain eq $live ? live_url() : dev_url(); -} - -sub new { - my ($class, $ref) = @_; - $ref ||= {}; - bless $ref, $class; - return $ref; -} - -sub new_from_xml { - my ($self, $pkg, $xmlfrag, $util) = @_; - my $obj = $pkg->new(ref $self ? { util => $self->util(),} : {}); - - if($util) { - $obj->util($util); - } - - $obj->_init_from_xml_node($xmlfrag); - return $obj; -} - -sub fields { - return (); -} - -sub primary_key { - my $self = shift; - return ($self->fields())[0]; -} - -sub util { - my ($self, $util) = @_; - if($util) { - $self->{util} = $util; - } - if (!$self->{util}) { - $self->{util} = npg::api::util->new(); - } - return $self->{util}; -} - -sub get { - my ($self, $field) = @_; - - $field = lc $field; - if($self->{$field}) { - return $self->{$field}; - } - if($self->{id}) { - $self->parse(); - } - return $self->{$field}; -} - -sub entity_name { - my $self = shift; - my $pkg = ref $self; - my ($name) = $pkg =~ /([^:]+)$/smx; - return $name; -} - -sub parse { - my $self = shift; - - if(!$self->{parsed}) { - if(!$self->{id}) { - carp q[Not going to parse - no id given]; - return; - } - - my $doc = $self->read(); - my $el = $doc->getElementsByTagName($self->entity_name())->[0]; - - if(!$el) { - return; - } - - $self->_init_from_xml_node($el); - - $self->{parsed}++; - } - - return; -} - -sub _init_from_xml_node { - my ($self, $el) = @_; - - my @descriptors = @{$el->getElementsByTagName('descriptor')}; - if (!@descriptors) {@descriptors= @{$el->getElementsByTagName('property')};} - - for my $desc (@descriptors) { - my $namec; - eval { - $namec = $desc->getElementsByTagName('parameter')->[0]->getFirstChild(); - } or do { - eval { - $namec = $desc->getElementsByTagName('name')->[0]->getFirstChild(); - } or do { - carp q{unable to obtain name via name or parameter}; - }; - }; - my $name = $namec?$namec->getData():undef; - $name = lc $name; - my $valuec = $desc->getElementsByTagName('value')->[0]->getFirstChild(); - my $value = $valuec?$valuec->getData():undef; - if (defined $value) { - chomp $value; - } - - $self->{$name} ||= []; - push @{$self->{$name}}, $value; - } - - for my $f ($self->fields()) { - my $ea = $el->getElementsByTagName($f); - if (scalar @{$ea} and $ea->[0]->getFirstChild()) { - $self->{$f} = $el->getElementsByTagName($f)->[0]->getFirstChild->getData(); - } - } - return; -} - -sub obj_uri { - my $self = shift; - return sprintf q(%s/%s), $self->service(), $self->{'id'}; -} - -sub read { ## no critic (ProhibitBuiltinHomonyms) - my $self = shift; - - if(exists $self->{read}) { - return $self->{read}; - } - - if(!$self->{id}) { - carp qq[@{[ref $self]} cannot read without an id]; - $self->{read} = undef; - return; - } - - my $obj_uri = $self->obj_uri(); - my $response_content = $self->util->request('text/xml')->make($obj_uri); - my $doc; - eval { - $doc = $self->util->parser->parse_string($response_content); - - } or do { - my $error_message = $response_content . qq{\n parsing $obj_uri\n\n}; - $error_message .= qq{This could be due to Sequencescape problems such as a dead mongrel node,\n}; - $error_message .= qq{as this response has come from the st::api modules.\n}; - $error_message .= qq{Please quote this in an email to seq-help\@sanger.ac.uk\n\n}; - - croak $error_message; - }; - - my $root = $doc->documentElement(); - my $e_name = $self->entity_name(); - my $r_name = $root->nodeName(); - - if($r_name ne $e_name) { - $self->{read} = undef; - return; - } - - $self->{read} = $doc; - return $doc; -} - -sub service { - my ($self) = @_; - my $path = $self->can(q{path}) ? $self->path() : q{}; - return join q[/], $self->lims_url, $path; -} - -1; -__END__ - -=head1 NAME - -st::api::base - a base class for st::api::* - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -=head1 SUBROUTINES/METHODS - -=head2 fields - returns empty array (all subclasses should have own fields method) - -=head2 primary_key - returns primary key for class model - -=head2 new - default constructor - - my $oDerived = ->new(); - - my $oDerived = ->new({key => value, ...}); - -=head2 new_from_xml - create and populate an st::api::* from a XML::LibXML::Element - - my $oObj = $oDerived->new_from_xml('st::api::', $oXMLElement); - -=head2 get - default 'get' accessor (see also Class::Accessor) - - my $val = $oDerived->get($sFieldName); - -=head2 entity_name - derived from package name, top-level XML entity to parse, similar to SQL table in npg::model:: - - my $entity_name = $oDerived->entity_name(); - -=head2 parse - default 'item' parsing. Invoked by default 'get' accessor. - - my $oDerived = ->new({'id' => $iId}); - $oDerived->parse(); - -=head2 read - default fetching and parsing for single entities - - my $oXMLFrag = $oDerived->read(); - -=head2 live_url - common part of URL for all live st services - - my $CommonLiveURLPart = $oDerived->live_url(); - -=head2 dev_url - common part of URL for all dev st services - - my $CommonDevURLPart = $oDerived->dev_url(); - -=head2 lims_url - common part of URL for all LIMs services, - transparently handles live/dev environment dependency - - my $CommonURLPart = $oDerived->lims_url(); - -=head2 service - current service URL - - my $sServiceURL = $oDerived->service(); - - $oDerived->service($sURL); - -=head2 obj_uri - URI from which current object can be sourced - - my $sServiceURL = $oDerived->obj_uri(); - -=head2 util - Get/set accessor for an npg::api::util object - - my $oSTUtil = $oSTObj->util(); - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item base - -=item Class::Accessor - -=item npg::api::util - -=item strict - -=item warnings - -=item Carp - -=item Readonly - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Roger Pettett, Ermp@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2008 GRL, by Roger Pettett -Copyright (C) 2011 GRL, by Marina Gourtovaia - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut diff --git a/lib/st/api/batch.pm b/lib/st/api/batch.pm deleted file mode 100644 index 69ad8b29..00000000 --- a/lib/st/api/batch.pm +++ /dev/null @@ -1,89 +0,0 @@ -######### -# Author: rmp -# Created: 2007-03-28 -# -package st::api::batch; -use base qw(st::api::base); -use strict; -use warnings; - -__PACKAGE__->mk_accessors(fields()); - -our $VERSION = '0'; - -sub path { - return q{batches}; -} - -sub fields { return qw(id); } - -1; -__END__ - -=head1 NAME - -st::api::batch - an interface to Sample Tracking batches - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -=head1 SUBROUTINES/METHODS - -=head2 fields - fields in this package - - These all have default get/set accessors. - - my @aFields = $oBatch->fields(); - my @aFields = ->fields(); - -=head2 path - object type specific path of object uri - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item base - -=item st::api::base - -=item strict - -=item warnings - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Roger Pettett, Ermp@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2008 GRL, by Roger Pettett - -This file is part of NPG. - -NPG is free software; you can redistribute it and/or modify it under -the terms of the GNU General Public License as published by the Free -Software Foundation; either version 2 of the License, or (at your -option) any later version. - -This program is distributed in the hope that it will be useful, but -WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see http://www.gnu.org/licenses/ . - -=cut diff --git a/lib/st/api/project.pm b/lib/st/api/project.pm deleted file mode 100644 index fe0b709f..00000000 --- a/lib/st/api/project.pm +++ /dev/null @@ -1,105 +0,0 @@ -######### -# Author: rmp -# Created: 2007-03-28 -# -package st::api::project; - -use strict; -use warnings; -use Carp; -use English qw{-no_match_vars}; - -use base qw(st::api::base); - -__PACKAGE__->mk_accessors(fields()); - -our $VERSION = '0'; - -sub path { - return q{projects}; -} - -sub fields { return qw( id name ); } - -sub project_cost_code { - my $self = shift; - my $proceject_cost_codes = $self->get('Project cost code') || []; - return $proceject_cost_codes ->[0]; -} - -1; -__END__ - -=head1 NAME - -st::api::project - an interface to a project - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -=head1 SUBROUTINES/METHODS - -=head2 fields - fields in this package - - These all have default get/set accessors. - - my @aFields = $oProject->fields(); - my @aFields = ->fields(); - -=head2 path - object type specific path of object uri - -=head2 project_cost_code - - my $project_cost_code = $oProject->project_cost_code; - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item base - -=item st::api::base - -=item strict - -=item warnings - -=item Carp - -=item English - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Roger Pettett, Ermp@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2010 GRL, by gq1 - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut diff --git a/lib/st/api/sample.pm b/lib/st/api/sample.pm deleted file mode 100644 index 83f87df6..00000000 --- a/lib/st/api/sample.pm +++ /dev/null @@ -1,230 +0,0 @@ -######### -# Author: rmp -# Created: 2007-03-28 - -package st::api::sample; - -use base qw(st::api::base); -use strict; -use warnings; -use Carp; - -__PACKAGE__->mk_accessors(fields()); - -our $VERSION = '0'; - -sub _parse_taxon_id { - my ($self, $taxon_id) = @_; - # sometimes taxon ids are floats ending with .0; it's a result of uploading data from - # Excel spreadsheets without checking the type. Safe to extract the integer part. - if ($taxon_id) { - my ($int_taxon_id) = $taxon_id =~ /^(\d+)\.0$/sxm; - if ($int_taxon_id) { - carp q[Sample ] . $self->id . qq[: taxon id is a float $taxon_id]; - return $int_taxon_id; - } - } - return $taxon_id; -} - -sub path { - return q{samples}; -} - -sub fields { return qw( id name gc-content organism scientific-rationale concentration consent_withdrawn ); } - -sub consent_withdrawn { - my $self = shift; - $self->parse(); - my $consent_withdrawn = $self->get( q(consent_withdrawn) ); - return $consent_withdrawn && $consent_withdrawn eq q{true}; -} - -sub description { - my $self = shift; - $self->parse(); - my $result = $self->get('Sample Description'); - return ref $result ? $result->[0] : $result; -} - -sub organism { - my $self = shift; - $self->parse(); - my $result = $self->get(q(organism)); - return ref $result ? $result->[0] : $result -} - -sub taxon_id { - my $self = shift; - $self->parse(); - return $self->_parse_taxon_id($self->get(q[TAXON ID])->[0]); -} - -sub common_name { - my $self = shift; - $self->parse(); - return $self->get(q[Common Name])->[0]; -} - -sub public_name { - my $self = shift; - $self->parse(); - return $self->get(q[Public Name])->[0]; -} - -sub accession_number { - my ( $self ) = @_; - my $a_n = $self->get( 'ENA Sample Accession Number' ) || []; - return $a_n->[0]; -} - -sub strain { - my $self = shift; - $self->parse(); - return $self->get(q[Strain])->[0]; -} - -sub reference_genome { - my $self = shift; - $self->parse(); - return ($self->get(q[Sample reference genome])||[])->[0] || ($self->get(q[Reference Genome])||[])->[0]; -} - -sub contains_nonconsented_human { - my ( $self ) = @_; - return $self->study()->contains_nonconsented_human(); -} -*contains_unconsented_human = \&contains_nonconsented_human; #Backward compat - -1; -__END__ - -=head1 NAME - -st::api::sample - an interface to sample lims - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -=head1 SUBROUTINES/METHODS - -=head2 fields - fields in this package - - These all have default get/set accessors. - - my @aFields = $oSample->fields(); - my @aFields = ->fields(); - -=head2 path - object type specific path of object uri - -=head2 organism - convenience method for ->get('Organism'); - - my $sOrganism = $oSample->organism(); - -=head2 strain - returns strain property - - my $strain = $oSample->strain(); - -=head2 common_name - returns common_name property - - my $common_name = $oSample->common_name(); - -=head2 public_name - returns public_name property - - my $public_name = $oSample->public_name(); - -=head2 accession_number - -returns the accession_number should it have been provided - - my $sAccessionNumber = $oSample->accession_number(); - -=head2 taxon_id - returns taxon_id property - - my $taxon_id = $oSample->taxon_id(); - -=head2 reference_genome - string indictating the reference sequence which should be used for alignments - - my $refernceString = $oStudy->reference_genome(); - -=head2 gc_content - return the 'GQ content' field for the sample - - my $GC_content = $oSample->gc_content(); - -=head2 rationale - return the sample's 'Scientific Rationale' field - - my $sci_rationale = $oSample->rationale(); - -=head2 concentration - return the sample's 'Concentration' field - - my $conc = $oSample->concentration(); - -=head2 priority - the 'Priority' field for the workflow_sample - - my $priority - $oWorkflowSample->priority(); - -=head2 study - st::api::study for this sample's study_id - - my $oStudy = $oSample->study(); - -=head2 contains_nonconsented_human - return the value for the study that this sample is from - - my $bContainsNonconsentedHuman = $oSample->contains_nonconsented_human(); - -=head2 contains_unconsented_human - (Backward compat) return the value for the study that this sample is from - - my $bContainsUnconsentedHuman = $oSample->contains_unconsented_human(); - -=head2 consent_withdrawn - boolean value indicating whether consent has been withdrawn for a sample containing human DNA - -=head2 description - sample description - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item base - -=item st::api::base - -=item strict - -=item warnings - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Roger Pettett, Ermp@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2008 GRL, by Roger Pettett - -This file is part of NPG. - -NPG is free software; you can redistribute it and/or modify it under -the terms of the GNU General Public License as published by the Free -Software Foundation; either version 2 of the License, or (at your -option) any later version. - -This program is distributed in the hope that it will be useful, but -WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU -General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see http://www.gnu.org/licenses/ . - -=cut diff --git a/lib/st/api/study.pm b/lib/st/api/study.pm deleted file mode 100644 index a57d213f..00000000 --- a/lib/st/api/study.pm +++ /dev/null @@ -1,268 +0,0 @@ -######### -# Author: gq1 -# Created: 2010-04-29 - -package st::api::study; - -use base qw(st::api::base); -use strict; -use warnings; -use List::MoreUtils qw/ uniq /; - -__PACKAGE__->mk_accessors(fields()); - -our $VERSION = '0'; - -sub path { - return q{studies}; -} - -sub fields { return qw( id name ); } - -sub separate_y_chromosome_data { - my $self = shift; - my $result = $self->get('Does this study require Y chromosome data to be separated from X and autosomal data before archival?') || []; - $result = $result->[0] || q[]; - return $result=~/yes|true|1/smix; -} - -sub contains_nonconsented_xahuman { - my $self = shift; - my $unconsented_xahuman = $self->get('Does this study require the removal of X chromosome and autosome sequence?') || []; - $unconsented_xahuman = $unconsented_xahuman->[0] || q[]; - return lc($unconsented_xahuman) eq q(yes); -} - -sub contains_nonconsented_human { - my $self = shift; - my $unconsented_human = $self->get('Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis?') || []; - $unconsented_human = $unconsented_human->[0] || q[]; - return lc($unconsented_human) eq q(yes); -} -*contains_unconsented_human = \&contains_nonconsented_human; #backward compat - -sub _emails_within_tag { - my ($self,$type)=@_; - if(not defined $type){ - $type=q{}; - } - my $ra=$self->{_emails}{$type}; - if ($ra){ - return $ra; - } - my $doc=$self->read(); - my @nl = ($doc); - if ($type) { - @nl = $doc->getElementsByTagName($type); - } - my $results=[]; - for my $n (@nl){ - for my $e ($n->getElementsByTagName(q(email))){ - my $email = $e->textContent(); - if($email){ - $email=~s/\a\s+//smx; - $email=~s/\s+\z//smx; - if($email){ - push @{$results},$email; - } - } - } - } - @{$results} = uniq sort @{$results}; - $self->{_emails}{$type}=$results; - return $results; -} - -sub email_addresses { - my $self = shift; - return $self->_emails_within_tag(); -} - -sub email_addresses_of_managers { - my $self = shift; - return $self->_emails_within_tag(q{managers}); -} - -sub email_addresses_of_followers { - my $self = shift; - return $self->_emails_within_tag(q{followers}); -} - -sub email_addresses_of_owners { - my $self = shift; - return $self->_emails_within_tag(q{owners}); -} - -sub reference_genome { - my $self = shift; - $self->parse(); - return ($self->get(q[Reference Genome])||[])->[0]; -} - -sub alignments_in_bam { - my $self = shift; - my $r = $self->get('Alignments in BAM'); - if( !defined $r || $r->[0] !~ m/false/smix ) { - return 1; - } - return; -} - -sub accession_number { - my ( $self ) = @_; - my $a_n = $self->get('ENA Study Accession Number') || []; - return $a_n->[0]; -} - -sub title { - my ( $self ) = @_; - my $title = $self->get('Title') || []; - return $title->[0]; -} - -sub description { - my ( $self ) = @_; - my $e = $self->get(q{Study description}); - my $d; - if (defined $e) { - $d = $e->[0]; - } - return $d ? $d : undef; -} - -sub data_access_group { - my ( $self ) = @_; - my $group = $self->get('Data access group') || []; - return $group->[0]; -} - -1; -__END__ - -=head1 NAME - -st::api::study - an interface to Sample Tracking studies - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -=head1 SUBROUTINES/METHODS - -=head2 fields - fields in this package - - These all have default get/set accessors. - - my @aFields = $oStudy->fields(); - my @aFields = ->fields(); - -=head2 path - object type specific path of object uri - -=head2 separate_y_chromosome_data - Does the study have associated samples in which there is Y human DNA data is not been consented for public release. - - my $split_y = $oStudy->separate_y_chromosome_data(); - -=head2 contains_nonconsented_human - Does the study have associated samples in which there is human DNA which has not been consented for release. - - my $do_not_release = $oStudy->contains_nonconsented_human(); - -=head2 contains_unconsented_human - (Backward compat) Does the study have associated samples in which there is human DNA which has not been consented for release. - -=head2 contains_nonconsented_xahuman - as contains_nonconsented_human, but specifically for the X chromosome and autosome parts - -=head2 email_addresses - arrayref of email addresses related to this study - - my $arEmailStrings = $oStudy->email_addresses(); - -=head2 email_addresses_of_followers - arrayref of email addresses of followers of this study - - my $arEmailStrings = $oStudy->email_addresses_of_followers(); - -=head2 email_addresses_of_managers - arrayref of email addresses of managers of this study - - my $arEmailStrings = $oStudy->email_addresses_of_managers(); - -=head2 email_addresses_of_owners - arrayref of email addresses of owners of this study - - my $arEmailStrings = $oProject->email_addresses_of_owners(); - -=head2 reference_genome - string indictating the reference sequence which should be used for alignments - - my $refernceString = $oStudy->reference_genome(); - -=head2 alignments_in_bam - are alignments wanted in BAM files produced for this study - - my $boolean = $oStudy->alignments_in_bam(); - -=head2 accession_number - -returns the accession number from sequencescape for this study - - my $sAccessionNumber = $oStudy->accession_number(); - -=head2 title - -returns the title for the study - - my $sTitle = $oStudy->title(); - -=head2 description - -returns text description of the study - - my $sDescription = $oStudy->description(); - -=head2 data_access_group - -returns group to which data access should be limited - - my $sGroup = $oStudy->data_access_group(); - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item base - -=item st::api::base - -=item strict - -=item warnings - -=item List::MoreUtils - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Guoying Qi, Egq1@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2010 GRL, by gq1 - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut diff --git a/t/30-api-request.t b/t/30-api-request.t deleted file mode 100644 index 04b0253e..00000000 --- a/t/30-api-request.t +++ /dev/null @@ -1,149 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 30; -use Test::Exception; -use Test::Deep; -use File::Temp qw/ tempdir /; -use File::Spec::Functions qw(catfile); -use File::Path qw(make_path ); -use HTTP::Request::Common; -use Test::MockObject; - -use st::api::batch; -use npg::api::util; -use st::api::sample; - -use t::useragent; -my $lims_url = q[http://sequencescape.psd.sanger.ac.uk]; -my $ua = t::useragent->new({ - is_success => 1, - mock => { - $lims_url.q{/batches/1027} => q{t/data/npg_api/st/batches/1027.xml}, - $lims_url.q{/batches/1826} => q{t/data/npg_api/st/batches/1826.xml}, - $lims_url.q{/samples/10014} => q{t/data/npg_api/st/samples/10014.xml}, - }, - }); - -use_ok('npg::api::request'); - -my $base_url = $npg::api::util::LIVE_BASE_URI; -my $VAR_NAME = q[]; -my $TEST_CACHE = q[t/data/npg_api]; - -{ - my $r = npg::api::request->new(); - isa_ok($r, 'npg::api::request'); - $VAR_NAME = $r->cache_dir_var_name; -} - -{ - is (npg::api::request->cache_dir_var_name, q[NPG_WEBSERVICE_CACHE_DIR], 'class attr for var name'); - is (npg::api::request->new()->cache_dir_var_name, q[NPG_WEBSERVICE_CACHE_DIR], 'class attr for var name works for an instance as well'); - is (npg::api::request->new()->cache_dir_var_name, q[NPG_WEBSERVICE_CACHE_DIR], 'class attr for var name works for an instance as well'); -} - -{ - my $r = npg::api::request->new(); - throws_ok { $r->make() } qr/Uri is not defined/, 'error if no uri given'; - throws_ok { $r->make(q[]) } qr/Uri is not defined/, 'error if an empty uri given'; - - local $ENV{$VAR_NAME} = q[/dome/non-existing]; - throws_ok { $r->make(q[dodo], q[GET]) } qr/Cache directory \/dome\/non-existing does not exist/, 'error when a cache directory does not exist'; - - local $ENV{$VAR_NAME} = q[Changes]; - throws_ok { $r->make(q[dodo], q[GET]) } qr/is not a directory/, 'error when a cache directory is not a directory'; -} - -{ - local $ENV{$VAR_NAME} = q[t]; - my $r = npg::api::request->new(); - - is( $r->_create_path($base_url.q{/run/1234.xml}), - q{t/npg/run/1234.xml}, q{npg path generated ok} ); - is( $r->_create_path($lims_url.q{/batches/6935.xml}), - q{t/st/batches/6935.xml}, q{st path created ok}); - is( $r->_create_path(q{http://news.bbc.co.uk/sport1/hi/football/world_cup_2010/matches/match_01}), - q{t/ext/sport1/hi/football/world_cup_2010/matches/match_01}, - q{external path generated ok} ); -} - -{ - my $r = npg::api::request->new(); - my $req = GET q[dodo]; - $r->_personalise_request($req); - is ($req->header(q[X-username]), getlogin, 'username set in the request header'); -} - -{ - my $util = npg::api::util->new({useragent => $ua, max_retries => 1,}); - my $sample_id = 10014; - ok (-e catfile($TEST_CACHE, q[st], q[samples], $sample_id . q[.xml]), 'test prerequisite OK'); - is ( st::api::sample->new({id => $sample_id, util => npg::api::util->new({useragent => $ua,}), })->name, q[104A_Sc_YPS128], 'sample fetched, name correct'); - - my $dir = tempdir( CLEANUP => 1 ); - local $ENV{$VAR_NAME} = $dir; - throws_ok { st::api::sample->new({id => $sample_id,})->name } qr/is not in the cache/, 'error when fetching from a cache a resource that is not there'; -} - -{ - my $util = npg::api::util->new({useragent => $ua, max_retries => 1,}); - my $batch_id = 1027; - my $url = catfile(q[st], q[batches], $batch_id . q[.xml]); - ok (-e catfile($TEST_CACHE, $url), 'test prerequisite OK'); - lives_ok {st::api::batch->new({id => $batch_id, util => $util,})->read()} 'batch retrieved'; - - my $dir = tempdir( CLEANUP => 1 ); - local $ENV{$VAR_NAME} = $dir; - throws_ok { st::api::batch->new({id => $batch_id, util => $util,})->read()} - qr/is not in the cache/, 'error when a resource is not in cache'; - - local $ENV{npg::api::request->save2cache_dir_var_name} = 1; - lives_ok { st::api::batch->new({util => $util, id => $batch_id})->read() } - 'call to request and save the resource lives'; - ok (-e catfile($dir, $url), 'batch xml saved to cache'); - - $batch_id = 1826; - $url = catfile(q[st], q[batches], $batch_id . q[.xml]); - ok (-e catfile($TEST_CACHE, $url), 'test prerequisite OK'); - lives_ok { st::api::batch->new({util => $util, id => $batch_id, })->read() } 'call to save a second batch lives'; - ok (-e catfile($dir, $url), 'second batch xml saved to cache'); -} - -{ - my $batch_id = 3022; - my $original = catfile($TEST_CACHE, q[st], q[batches], $batch_id . q[.xml]); - ok (-e $original, 'test prerequisite OK'); - my $batch1 = st::api::batch->new({id => $batch_id,}); - - my $cache = tempdir( CLEANUP => 1 ); - local $ENV{$VAR_NAME} = $cache; - make_path catfile($cache, q[st], q[batches]); - my $copy = catfile($cache, q[st], q[batches], $batch_id . q[.xml]); - `cp $original $copy`; - ok (-e $copy, 'test prerequisite OK'); - my $batch2 = st::api::batch->new({id => $batch_id,}); - cmp_deeply ($batch1, $batch2, 'the same object returned from cache and test repository'); -} - - -{ - my $content = q[Run 2888 tagged]; - - my $mockUA = Test::MockObject->new(); - $mockUA->fake_new(q{LWP::UserAgent}); - - my $fake_response = HTTP::Response->new(200, '200 Ok', undef, "$content"); - $mockUA->set_always('request', $fake_response); - $mockUA->set_always('timeout', 60); - $mockUA->set_always('agent', q[npg::api::request]); - $mockUA->set_always('env_proxy', q[]); - my $returned; - lives_ok {$returned = npg::api::request->new()->make($base_url.q[/run/4913], q[POST])} 'post request lives'; - is ($returned, $content, 'correct response returned'); - - local $ENV{$VAR_NAME} = q[t]; - throws_ok {npg::api::request->new()->make($base_url.q[/run/4913], q[POST])} - qr/POST requests cannot use cache:/, 'post request croaks if cache is set'; -} - -1; diff --git a/t/30-api-util.t b/t/30-api-util.t deleted file mode 100644 index 5b5a4dd1..00000000 --- a/t/30-api-util.t +++ /dev/null @@ -1,45 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 10; - -use_ok('npg::api::util'); - -{ - my $util = npg::api::util->new({ - base_uri => '/foo', - useragent => 'foo', - parser => 'foo', - }); - is($util->base_uri(), '/foo', 'base url set explicitly'); - is($util->useragent(), 'foo'); - is($util->parser(), 'foo'); -} - -{ - my $util = npg::api::util->new(); - isa_ok($util->useragent(), 'LWP::UserAgent'); - isa_ok($util->parser(), 'XML::LibXML'); - isa_ok($util->request(), 'npg::api::request'); -} - -{ - my $util = npg::api::util->new(); - is ($util->base_uri(), 'http://sfweb.internal.sanger.ac.uk:9000/perl/npg', - 'live url if the dev env variable not set'); -} - -{ - local $ENV{dev} = q[dev]; - my $util = npg::api::util->new(); - is ($util->base_uri(), 'http://sf2-farm-srv2.internal.sanger.ac.uk:9010/perl/npg', - 'dev url if the dev env variable is set to dev'); -} - -{ - local $ENV{dev} = q[test]; - my $util = npg::api::util->new(); - is ($util->base_uri(), 'http://sfweb.internal.sanger.ac.uk:9000/perl/npg', - 'live url if the dev env. variable is set to test'); -} - -1; diff --git a/t/40-st-base.t b/t/40-st-base.t deleted file mode 100644 index 1082b070..00000000 --- a/t/40-st-base.t +++ /dev/null @@ -1,25 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 10; - -use_ok('st::api::base'); - -{ - my $base = st::api::base->new(); - isa_ok($base, 'st::api::base'); - like($base->live_url(), qr/sequencescape[.]psd/, 'live_url'); - like($base->dev_url(), qr/dev\.psd/, 'dev_url'); - is((scalar $base->fields()), undef, 'no default fields'); - is($base->primary_key(), undef, 'no default pk'); - - is($base->lims_url(), $base->live_url(),'live url returned'); - is($base->service(), $base->live_url() . q[/],'live url returned'); - { - local $ENV{'dev'} = 'some'; - is($base->lims_url(), $base->dev_url(), 'dev url returned'); - is($base->service(), $base->dev_url() . q[/],'dev url returned'); - } - -} - -1; diff --git a/t/40-st-batch.t b/t/40-st-batch.t deleted file mode 100644 index caaa520e..00000000 --- a/t/40-st-batch.t +++ /dev/null @@ -1,9 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 2; - -use_ok('st::api::batch'); -my $batch = st::api::batch->new(); -isa_ok($batch, 'st::api::batch'); - -1; diff --git a/t/40-st-project.t b/t/40-st-project.t deleted file mode 100644 index b2df1bec..00000000 --- a/t/40-st-project.t +++ /dev/null @@ -1,22 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 6; - -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; - -use_ok('st::api::project'); - -{ - my $project = st::api::project->new(); - isa_ok($project, 'st::api::project'); - is($project->project_cost_code(), undef, 'no project code returned with no data'); -} - -{ - my $project = st::api::project->new({id => 429,}); - is ($project->id, 429, 'project id'); - is ($project->name, '3C and HiC of Plasmodium falciparum IT', 'project name'); - is ($project->project_cost_code, 'S0701', 'project cost code'); -} - -1; diff --git a/t/40-st-sample.t b/t/40-st-sample.t deleted file mode 100644 index dc9c6125..00000000 --- a/t/40-st-sample.t +++ /dev/null @@ -1,42 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 23; - -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; - -use_ok('st::api::sample'); - -my $sample = st::api::sample->new({id => 1750,}); -isa_ok($sample, 'st::api::sample', 'isa ok'); - -is($sample->id(), 1750, 'id ok'); -is($sample->name(), 'p242-NspI-PCR 2A2', 'name fetched ok'); -is($sample->organism(), 'Danio rerio', 'organism field fetched ok'); - -my $sample_description = 'AB GO (grandmother) of the MGH meiotic cross. The same DNA was split into three aliquots (of which this is reaction A), processed in parallel, they were: NspI cut, ligated with modified recuttable adaptor (ATTATGAGCACGACAGACGCCTGATCTRCATG and YAGATCAGGCGTCTGTCGTGCTCATAA), and PCR amplified.'; -is($sample->description(), $sample_description, 'Description field fetched ok'); - -$sample = st::api::sample->new({id => 7283,}); -cmp_ok($sample->id(), q(==), 7283, 'id ok'); -cmp_ok($sample->name(), q(eq), 'PD3918a', 'name fetched ok'); -cmp_ok($sample->organism(), q(eq), 'Human', 'organism fetched ok'); -is($sample->taxon_id(), 9606, 'taxon ID'); -is($sample->common_name(), 'Homo sapiens', 'common name'); -is($sample->public_name(), undef, 'public name undefined'); -is($sample->strain(), undef, 'strain undefined'); -is($sample->reference_genome(), undef, 'sample reference genome undefined'); - -$sample = st::api::sample->new({id => 10881,}); -is($sample->organism(), 'Salmonella enterica Java', 'organism fetched ok'); -is($sample->taxon_id(), '224729', 'TAXON ID fetched ok'); -is($sample->common_name(), 'Salmonella enterica subsp. enterica serovar Java', 'Common Name fetched ok'); -is($sample->public_name(), 'H083280501', 'public name fetched ok'); -is($sample->strain(), 'S java', 'strain fetched ok'); - -is( st::api::sample->new({id => 1121926,})->reference_genome(), 'Schistosoma_mansoni (20100601)', 'ref genome'); - -ok( !st::api::sample->new({id => 11036,})->consent_withdrawn(), q{consent not withdrawn for sample 11036} ); -ok( !st::api::sample->new({id => 1121926,})->consent_withdrawn(), q{consent withdrawn not given for sample 1121926} ); -ok( st::api::sample->new({id => 1299723,})->consent_withdrawn(), q{consent withdrawn for sample 1299723} ); - -1; diff --git a/t/40-st-study.t b/t/40-st-study.t deleted file mode 100644 index d204ba27..00000000 --- a/t/40-st-study.t +++ /dev/null @@ -1,63 +0,0 @@ -use strict; -use warnings; -use Test::More tests => 28; -use Test::Exception; - -local $ENV{NPG_WEBSERVICE_CACHE_DIR} = 't/data/st_api_lims_new'; - -use_ok('st::api::study'); - -{ - my $study = st::api::study->new(); - isa_ok($study, 'st::api::study'); -} - -{ - my $study = st::api::study->new({id => 11}); - is($study->name(), q{Trypanosoma brucei}, 'correct study name'); - ok(!$study->contains_unconsented_human(), 'study 11 no unconsented human'); - is($study->reference_genome, 'dodo', 'reference genome '); - ok( !$study->data_access_group(), 'no data access group set'); -} - -{ - my $study = st::api::study->new({id => 162,}); - ok($study->contains_unconsented_human() , 'Marked with unconsented human'); #backward compat - ok($study->contains_nonconsented_human() , 'Marked with nonconsented human'); - is_deeply($study->email_addresses,[qw(chc@sanger.ac.uk deh@sanger.ac.uk hss@sanger.ac.uk jm15@sanger.ac.uk nds@sanger.ac.uk sh16@sanger.ac.uk tfelt@sanger.ac.uk)],'All email addresses'); - is_deeply($study->email_addresses_of_managers,[qw(chc@sanger.ac.uk jm15@sanger.ac.uk nds@sanger.ac.uk)],'Managers email addresses'); - is_deeply($study->email_addresses_of_followers,[qw(chc@sanger.ac.uk deh@sanger.ac.uk hss@sanger.ac.uk sh16@sanger.ac.uk)],'Followers email addresses'); - is_deeply($study->email_addresses_of_owners,[qw(tfelt@sanger.ac.uk)],'Owners email addresses'); - is($study->reference_genome, undef, 'reference genome undefined for study 162'); - - my $study2 = st::api::study->new({id => 292,}); - ok(!$study2->contains_unconsented_human() , 'Not marked with unconsented human'); #backward compat - ok(!$study2->contains_nonconsented_human() , 'Not marked with nonconsented human'); - lives_and {ok(!$study2->contains_nonconsented_xahuman()) } 'Not marked with nonconsented X and autosome human'; - - my $study3 = st::api::study->new({id => 2278,}); - lives_and {ok($study3->contains_nonconsented_xahuman()) } 'Marked with nonconsented X and autosome human'; -} - -{ - my $study = st::api::study->new({id => 11,}); - ok($study->alignments_in_bam, 'alignments in BAM when no corresponding XML in study'); - $study = st::api::study->new({id => 700,}); - ok($study->alignments_in_bam, 'alignments in BAM when true in corresponding XML in study'); - is( $study->title(), 'hifi test', q{title} ); - is( $study->name(), 'Kapa HiFi test', 'study name'); - is( $study->accession_number(), undef, q{no accession obtained} ); - $study = st::api::study->new({id => 701,}); - ok(! $study->alignments_in_bam, 'no alignments in BAM when false in corresponding XML in study'); - is( $study->title(), 'Genetic variation in Kuusamo', q{title obtained} ); - is( $study->accession_number(), 'EGAS00001000020', q{accession obtained} ); - ok(! $study->separate_y_chromosome_data, 'separate_y_chromosome_data false for study'); - is( $study->data_access_group(), 'kuusamo', 'data access group set'); -} - -{ - my $study = st::api::study->new({id => 2693}); - ok($study->separate_y_chromosome_data, 'separate_y_chromosome_data true for study'); -} - -1; From e6505a4510aa544845ec8bc5e80380f6b0a9ebc4 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 12 Oct 2023 17:02:48 +0100 Subject: [PATCH 08/35] Deleted low value live tests --- MANIFEST | 2 - lib/npg_testing/intweb.pm | 135 -------------------------------------- t/90-reference.t | 94 -------------------------- 3 files changed, 231 deletions(-) delete mode 100644 lib/npg_testing/intweb.pm delete mode 100644 t/90-reference.t diff --git a/MANIFEST b/MANIFEST index 5dad2d69..e6da38b9 100644 --- a/MANIFEST +++ b/MANIFEST @@ -186,7 +186,6 @@ lib/npg/view/user2usergroup.pm lib/npg/view/usergroup.pm lib/npg_testing/db.pm lib/npg_testing/html.pm -lib/npg_testing/intweb.pm lib/npg_tracking/daemon.pm lib/npg_tracking/data/bait.pm lib/npg_tracking/data/bait/find.pm @@ -416,7 +415,6 @@ t/70-bin-npg_status2file.t t/80-npg_tracking-report-events.t t/80-npg_tracking-report-event2followers.t t/80-npg_tracking-report-event2subscribers.t -t/90-reference.t t/data/schema.txt t/data/090414_IL24_2726.tar.bz2 t/data/dbic_fixtures/000-Designation.yml diff --git a/lib/npg_testing/intweb.pm b/lib/npg_testing/intweb.pm deleted file mode 100644 index a85f153c..00000000 --- a/lib/npg_testing/intweb.pm +++ /dev/null @@ -1,135 +0,0 @@ -package npg_testing::intweb; - -use strict; -use warnings; -use Carp; -use English qw{-no_match_vars}; -use Exporter; -use LWP::UserAgent; -use HTTP::Request::Common; -use npg::api::util; - -our $VERSION = '0'; - -=head1 NAME - -npg_testing::intweb - -=head1 VERSION - -=head1 SYNOPSIS - -=head1 DESCRIPTION - -A collection of functions to test the availability of internal Sanger sites - -=head1 SUBROUTINES/METHODS - -=cut - -Readonly::Scalar our $LWP_TIMEOUT => 60; -Readonly::Scalar our $MAX_NUM_ATTEMPTS => 2; - -## no critic (ProhibitExplicitISA) -our @ISA = qw(Exporter); -our @EXPORT_OK = qw(npg_is_accessible); - -sub _attempt_request { - my ($request, $ua) = @_; - - my $response; - eval { - $response = $ua->request($request); - 1; - } or do { - carp $EVAL_ERROR; - return 0; - }; - if ($response->is_success) { - return 1; - } else { - carp $response->status_line(); - } - return 0; -} - -=head2 npg_is_accessible - -Tests whether it is possible to access NPG home page - -=cut -sub npg_is_accessible { - my $url = shift; - - $url ||= $npg::api::util::LIVE_BASE_URI; - my $request = GET $url; - my $ua = LWP::UserAgent->new(); - $ua->agent("npg_testing::intweb $VERSION"); - $ua->timeout($LWP_TIMEOUT); - $ua->env_proxy(); - - my $count = 0; - my $result = 0; - while ($count < $MAX_NUM_ATTEMPTS && !$result) { - $result = _attempt_request($request, $ua); - $count++; - } - return $result; -} - -1; -__END__ - -=head1 DIAGNOSTICS - -=head1 CONFIGURATION AND ENVIRONMENT - -=head1 DEPENDENCIES - -=over - -=item warnings - -=item strict - -=item Carp - -=item English - -=item Exporter - -=item LWP::UserAgent - -=item HTTP::Request::Common - -=back - -=head1 INCOMPATIBILITIES - -=head1 BUGS AND LIMITATIONS - -=head1 AUTHOR - -Marina Gourtovaia Emg8@sanger.ac.ukE - -=head1 LICENSE AND COPYRIGHT - -Copyright (C) 2010 GRL, by Marina Gourtovaia - -This file is part of NPG. - -NPG is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . - -=cut - diff --git a/t/90-reference.t b/t/90-reference.t deleted file mode 100644 index 33441138..00000000 --- a/t/90-reference.t +++ /dev/null @@ -1,94 +0,0 @@ -package reference; - -use strict; -use warnings; -use Test::More tests => 22; -use Test::Exception; -use npg_testing::intweb qw(npg_is_accessible); - -use_ok('npg_tracking::data::reference'); -use_ok('npg_tracking::data::bait'); -use npg_tracking::data::reference::list; - -my $REP_ROOT=$npg_tracking::data::reference::list::REP_ROOT; -my $PHIX_FILE=$REP_ROOT.q{references/PhiX/Sanger-SNPs/all/fasta/phix_unsnipped_short_no_N.fa}; - -{ -SKIP: { - - if (!npg_is_accessible()) { - skip 'Internal Sanger website is not accessible', 20; - } - if (!-e $REP_ROOT) { - skip 'reference repository is not accessible', 20; - } - my $r = npg_tracking::data::reference->new(id_run => 4354,position=>1); - is(join(q[ ], @{$r->refs}), - $REP_ROOT . q[references/Salmonella_enterica/Typhimurium_LT2/all/fasta/Salmonella_typimurium_LT2.fasta], - 'reference for run 4354 lane 1'); - - $r = npg_tracking::data::reference->new(id_run => 4350,position=>5); - is(join(q[ ], @{$r->refs}), - $REP_ROOT . q[references/Neisseria_meningitidis/MC58/all/fasta/N_meningitidis_MC58.fasta], - 'reference for run 4350 lane 5'); - - $r = npg_tracking::data::reference->new(id_run => 4415,position=>4); - is(join(q[ ], @{$r->refs}), - $PHIX_FILE, - 'reference for run 4415 lane 4'); - - $r = npg_tracking::data::reference->new(id_run => 4710,position=>3); - my @refs = @{$r->refs}; - is (scalar @refs, 1, 'one ref for run 4710 lane 3'); - my @expected = $REP_ROOT . qw{ - references/Human_herpesvirus_4/Wild_type/all/fasta/Hhv4_wild_type.fasta - }; - is(join(q[ ], sort @refs), join(q[ ], @expected), 'reference for run 4710 lane 3'); - - $r = npg_tracking::data::reference->new(id_run => 5082, position=>6); - is (scalar @{$r->refs}, 0, 'no refs for run 5082 lane 6'); - $r = npg_tracking::data::reference->new(id_run => 5082,position=>4); - is(join(q[ ], @{$r->refs}), - $PHIX_FILE, - 'reference for run 4415 lane 4'); - - - $r = npg_tracking::data::reference->new(id_run => 4784,position=>8); - is (scalar @{$r->refs}, 0, 'no refs for run 4784 position 8'); - - $r = npg_tracking::data::reference->new(id_run => 5175,position=>1); - @refs = @{$r->refs}; - is(join(q[ ], @refs), - $REP_ROOT . q[references/Streptococcus_pneumoniae/ATCC_700669/all/fasta/S_pneumoniae_700669.fasta], - 'reference for run 5175 lane 1 through the reference genome field'); - - $r = npg_tracking::data::reference->new(id_run => 5970,position=>1); - is ($r->refs->[0], $REP_ROOT . 'references/Anopheles_gambiae/PEST/all/fasta/agambiae.CHROMOSOMES-PEST.AgamP3.fasta', 'lane refs'); - - $r = npg_tracking::data::reference->new(id_run => 5970,position=>1, tag_index=>168); - throws_ok {$r->refs} qr/No plexes defined for lane 1 in batch 9659/, 'error if using tag_index 168 in the contex of not-pool library'; - $r = npg_tracking::data::reference->new(id_run => 5970,position=>1, for_spike => 1); - is ($r->refs->[0], $PHIX_FILE, 'spiked phix ref'); - $r = npg_tracking::data::reference->new(id_run => 5970,position=>6, tag_index=>888); - is ($r->refs->[0], $PHIX_FILE, 'spiked phix ref'); - - $r = npg_tracking::data::reference->new(id_run => 5970,position=>4); - is ($r->refs->[0], $PHIX_FILE, 'control phix ref'); - - $r = npg_tracking::data::reference->new(id_run => 6009,position=>1); - is ($r->refs->[0], $REP_ROOT . 'references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta', 'lane ref from the correct study'); - - $r = npg_tracking::data::reference->new(id_run => 6009,position=>7, tag_index=>7); - is ($r->refs->[0], $REP_ROOT . 'references/Homo_sapiens/1000Genomes/all/fasta/human_g1k_v37.fasta', 'tag ref from the correct study'); - - is(npg_tracking::data::bait->new(id_run=>8043, position=>3, tag_index=>1)->bait_path, - $r->bait_repository . '/Human_all_exon_50MB/1000Genomes_hs37d5', 'baits path'); - - lives_ok {$r->repository_contents} 'repository listing performed'; - my $report; - lives_ok {$report = $r->report} 'report generated'; - #diag $report; - lives_ok {$report = $r->short_report} 'short report generated'; - #diag $report; -} -} From eeb13a143cd734c93fe39508a5e136cdeb073d92 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 12 Oct 2023 21:52:21 +0100 Subject: [PATCH 09/35] Removed LIMS XML test fixtures --- MANIFEST | 506 -- t/data/npg_api/st/batches/1027.xml | 55 - t/data/npg_api/st/batches/13861.xml | 746 -- t/data/npg_api/st/batches/14601.xml | 607 -- t/data/npg_api/st/batches/1536.xml | 62 - t/data/npg_api/st/batches/16442.xml | 503 -- t/data/npg_api/st/batches/1826.xml | 62 - t/data/npg_api/st/batches/266.xml | 62 - t/data/npg_api/st/batches/3022.xml | 68 - t/data/npg_api/st/batches/3748.xml | 55 - t/data/npg_api/st/batches/4861.xml | 617 -- t/data/npg_api/st/batches/5298.xml | 63 - 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index e6da38b9..346e5a4b 100644 --- a/MANIFEST +++ b/MANIFEST @@ -508,49 +508,6 @@ t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/120110_M00119_0068_AMS0002022- t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/120110_M00119_0068_AMS0002022-00300/SampleSheet.csv t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/160408_HS31_19395_B_H5MMFADXY/Data/Intensities/config.xml t/data/long_info/nfs/sf20/ILorHSany_sf20/incoming/160408_HS31_19395_B_H5MMFADXY/RunInfo.xml -t/data/npg_api/ext/xml.xml -t/data/npg_api/st/batches/1027.xml -t/data/npg_api/st/batches/13861.xml -t/data/npg_api/st/batches/14601.xml -t/data/npg_api/st/batches/1536.xml -t/data/npg_api/st/batches/16442.xml -t/data/npg_api/st/batches/1826.xml -t/data/npg_api/st/batches/266.xml -t/data/npg_api/st/batches/3022.xml -t/data/npg_api/st/batches/3748.xml -t/data/npg_api/st/batches/4861.xml -t/data/npg_api/st/batches/5298.xml -t/data/npg_api/st/batches/5305.xml -t/data/npg_api/st/samples/10014.xml 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-t/data/npg_api/st/studies/578.xml -t/data/npg_api_run/npg/run/604.xml -t/data/npg_api_run/npg/run/636.xml t/data/pipeline_config/study_config_present/product_release.yml t/data/pipeline_config/study_config_absent/product_release.yml t/data/pipeline_config/study_config_tertiary_present/product_release.yml @@ -677,22 +634,6 @@ t/data/repos1/references/Plasmodium_falciparum/3D7/all/fasta/MAL.version2.1.4.fa t/data/repos1/references/Salmonella_pullorum/449_87/all/fasta/Salmonella_pullorum_449_87.fasta t/data/repos1/references/Strongyloides_ratti/20100601/all/fasta/S_ratti_010610.fa t/data/repos1/references/SARS-CoV-2/MN908947.3/all/fasta/MN908947.3.fa -t/data/repos1/st/batches/16442.xml -t/data/repos1/st/batches/16467.xml -t/data/repos1/st/batches/25539.xml -t/data/repos1/st/batches/25715.xml -t/data/repos1/st/samples/1327533.xml -t/data/repos1/st/samples/1327535.xml -t/data/repos1/st/samples/1327539.xml -t/data/repos1/st/samples/1382839.xml -t/data/repos1/st/samples/1807468.xml -t/data/repos1/st/samples/1830658.xml -t/data/repos1/st/studies/2072.xml -t/data/repos1/st/studies/2910.xml -t/data/request/npg/run/1234.xml -t/data/request/npg/run_status.xml -t/data/request/npg/run_status_dict.xml -t/data/request/st/assets/50801.xml t/data/run_info/runInfo.hiseq4000.single.twoind.xml t/data/run_info/runInfo.hiseq4000.xml t/data/run_info/runInfo.hiseq.rr.single.xml @@ -741,454 +682,8 @@ t/data/samplesheet/miseq_extended.csv t/data/samplesheet/multilane.csv t/data/samplesheet/novaseq_multirun.csv t/data/samplesheet/samplesheet_47539.csv -t/data/st_api_lims_new/st/assets/3033734.xml -t/data/st_api_lims_new/st/assets/3111688.xml -t/data/st_api_lims_new/st/batches/12141.xml -t/data/st_api_lims_new/st/batches/12378.xml -t/data/st_api_lims_new/st/batches/13410.xml -t/data/st_api_lims_new/st/batches/17763.xml -t/data/st_api_lims_new/st/batches/22061.xml -t/data/st_api_lims_new/st/batches/22829.xml -t/data/st_api_lims_new/st/projects/429.xml 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93 - GCACTGTC - 6 - - - - - - 94 - GCTAACTC - 6 - - - - - - 95 - GATTCATC - 6 - - - - - - 96 - GTCTTGGC - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 85 - GAGGATGG - 6 - - - - - - 86 - GTTGTCGG - 6 - - - - - - 87 - GGATTAGG - 6 - - - - - - 88 - GATAGAGG - 6 - - - - - - 89 - GTGTGTCG - 6 - - - - - - 90 - GCAATCCG - 6 - - - - - - 91 - GACCTTAG - 6 - - - - - - 92 - GCCTGTTC - 6 - - - - - - 93 - GCACTGTC - 6 - - - - - - 94 - GCTAACTC - 6 - - - - - - 95 - GATTCATC - 6 - - - - - - 96 - GTCTTGGC - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - 41 - TCCAGTCG - 6 - - - - - - 42 - TGTATGCG - 6 - - - - - - 43 - TCATTGAG - 6 - - - - - - 44 - TGGCTCAG - 6 - - - - - - 45 - TATGCCAG - 6 - - - - - - 46 - TCAGATTC - 6 - - - - - - 47 - TACTAGTC - 6 - - - - - - 48 - TTCAGCTC - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 61 - TGCTGATA - 6 - - - - - - 62 - TAGACGGA - 6 - - - - - - 63 - TGTGAAGA - 6 - - - - - - 64 - TCTCTTCA - 6 - - - - - - 65 - TTGTTCCA - 6 - - - - - - 66 - TGAAGCCA - 6 - - - - - - 67 - TACCACCA - 6 - - - - - - 68 - TGCGTGAA - 6 - - - - - - 69 - GGTGAGTT - 6 - - - - - - 70 - GATCTCTT - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - diff --git a/t/data/npg_api/st/batches/14601.xml b/t/data/npg_api/st/batches/14601.xml deleted file mode 100644 index 00adaef2..00000000 --- a/t/data/npg_api/st/batches/14601.xml +++ /dev/null @@ -1,607 +0,0 @@ - - - 14601 - started - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - diff --git a/t/data/npg_api/st/batches/1536.xml b/t/data/npg_api/st/batches/1536.xml deleted file mode 100644 index e21fbc4e..00000000 --- a/t/data/npg_api/st/batches/1536.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - 1536 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/batches/16442.xml b/t/data/npg_api/st/batches/16442.xml deleted file mode 100644 index bd744826..00000000 --- a/t/data/npg_api/st/batches/16442.xml +++ /dev/null @@ -1,503 +0,0 @@ - - - 16442 - released - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - 3 - TTAGGC - 3 - - - Fox bait - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - - 7 - CAGATC - 3 - - - - Human all exon 50MB - - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - - 168 - ACAACGCAAT - - 6 - - - - - - - - - - 5 - ACAGTG - 3 - - - Human all exon 50MB - - - - - - - 6 - GCCAAT - 3 - - - - Human all exon 50MB - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - 1 - ATCACG - - 3 - - - Human all exon 50MB - - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - - 7 - CAGATC - 3 - - - - Human all exon 50MB - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - 4 - TGACCA - - 3 - - - Human all exon 50MB - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - 5 - - ACAGTG - 3 - - - Human all exon 50MB - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - 6 - - GCCAAT - 3 - - - Mouse custom bait for Bronx Waltzer - - - - - - - 7 - CAGATC - 3 - - - - Mouse custom bait for Bronx Waltzer - - - - - - 8 - - ACTTGA - 3 - - - Mouse custom bait for Bronx Waltzer - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - 1 - - ATCACG - 3 - - - Mouse all exon - - - - - - - 2 - CGATGT - 3 - - - - Mouse all exon - - - - - - 3 - - TTAGGC - 3 - - - Mouse all exon - - - - - - - 4 - TGACCA - 3 - - - - Mouse all exon - - - - - - 5 - - ACAGTG - 3 - - - Mouse all exon - - - - - - - 6 - GCCAAT - 3 - - - - Mouse all exon - - - - - - 7 - - CAGATC - 3 - - - Mouse all exon - - - - - - - 8 - ACTTGA - 3 - - - - Mouse all exon - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - - 1 - ATCACG - 3 - - - - Mouse all exon - - - - - - - 2 - CGATGT - 3 - - - Mouse all exon - - - - - - - 3 - TTAGGC - 3 - - - - Mouse all exon - - - - - - - 4 - TGACCA - 3 - - - Mouse all exon - - - - - - - 5 - ACAGTG - 3 - - - - Mouse some exon - - - - - - - 6 - GCCAAT - 3 - - - Mouse all exon - - - - - - - - - 168 - ACAACGCAAT - - 6 - - - - - - - diff --git a/t/data/npg_api/st/batches/1826.xml b/t/data/npg_api/st/batches/1826.xml deleted file mode 100644 index 1b2d7a8f..00000000 --- a/t/data/npg_api/st/batches/1826.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - 1826 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/batches/266.xml b/t/data/npg_api/st/batches/266.xml deleted file mode 100644 index 617746d3..00000000 --- a/t/data/npg_api/st/batches/266.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - 266 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/batches/3022.xml b/t/data/npg_api/st/batches/3022.xml deleted file mode 100644 index c57d0da9..00000000 --- a/t/data/npg_api/st/batches/3022.xml +++ /dev/null @@ -1,68 +0,0 @@ - - - 3022 - released - - - - - - Mouse all exon - - - - - - - - - - - - - - - - - - - - - - - - Mouse all exon - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/batches/3748.xml b/t/data/npg_api/st/batches/3748.xml deleted file mode 100644 index 258c7e24..00000000 --- a/t/data/npg_api/st/batches/3748.xml +++ /dev/null @@ -1,55 +0,0 @@ - - - 3748 - started - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/batches/4861.xml b/t/data/npg_api/st/batches/4861.xml deleted file mode 100644 index 8fdd3968..00000000 --- a/t/data/npg_api/st/batches/4861.xml +++ /dev/null @@ -1,617 +0,0 @@ - - - 4861 - released - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - - - - - 1 - - 1 - - - - - - 2 - - 1 - - - - - - 3 - - 1 - - - - - - 4 - - 1 - - - - - - 5 - - 1 - - - - - - 6 - - 1 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - 12 - CTTGTA - 3 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - 12 - CTTGTA - 3 - - - - - - - diff --git a/t/data/npg_api/st/batches/5298.xml b/t/data/npg_api/st/batches/5298.xml deleted file mode 100644 index 95a6c4a3..00000000 --- a/t/data/npg_api/st/batches/5298.xml +++ /dev/null @@ -1,63 +0,0 @@ - - - 5298 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/batches/5305.xml b/t/data/npg_api/st/batches/5305.xml deleted file mode 100644 index 20b20ab7..00000000 --- a/t/data/npg_api/st/batches/5305.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - 5305 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api/st/samples/10014.xml b/t/data/npg_api/st/samples/10014.xml deleted file mode 100644 index e9942b41..00000000 --- a/t/data/npg_api/st/samples/10014.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 10014 - 104A_Sc_YPS128 - 390 - - - Phenotype - - - - Sample purified - - - - TAXON ID - 4932 - - - Country of origin - - - - Treatment - - - - Time Point - - - - Date of sample extraction - - - - Sample Description - - - - ENA Sample Accession Number - ERS016989 - - - Common Name - Saccharomyces cervisiae - - - Gender - - - - Mother - - - - Ethnicity - - - - Compound - - - - Cell Type - - - - Age - - - - Genotype - - - - Volume (µl) - - - - Dose - - - - Organism Part - - - - Growth Condition - - - - Concentration - - - - Public Name - 104A_Sc_YPS128 - - - Subject - - - - RNAi - - - - Concentration determind by - - - - Is re-submitted? - - - - DNA source - - - - Sample extraction method - - - - Disease - - - - Sibling - - - - Strain - - - - Cohort - - - - Immunoprecipitate - - - - Disease State - - - - Sample storage conditions - - - - Sample type - - - - Date of sample collection - - - - Developmental Stage - - - - Purification method - - - - Sample Visibility - Public - - - GC content - Neutral - - - Father - - - - Plate - - - - Geographical region - - - - Replicate - - - - Organism - S. cerevisiae - - - Reference Genome - - - - - - - - - - - - - 390 - diff --git a/t/data/npg_api/st/samples/1240077.xml b/t/data/npg_api/st/samples/1240077.xml deleted file mode 100644 index 6aef889e..00000000 --- a/t/data/npg_api/st/samples/1240077.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1240077 - PA0186-C - 578 - false - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 5833 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - ERS042050 - - - Strain - - - - GC content - High AT - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Age - - - - Sample Description - - - - Common Name - Plasmodium falciparum - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - 9790 - - - Gender - - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - malaria parasite P. falciparum - - - Reference Genome - - - - - - - - - - - - - - - 578 - diff --git a/t/data/npg_api/st/samples/1240078.xml b/t/data/npg_api/st/samples/1240078.xml deleted file mode 100644 index 1cbb4f41..00000000 --- a/t/data/npg_api/st/samples/1240078.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1240078 - PA0196-C - 578 - false - - - Organism - malaria parasite P. falciparum - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - High AT - - - Gender - - - - DNA source - Genomic - - - Public Name - 9800 - - - Common Name - Plasmodium falciparum - - - Strain - - - - TAXON ID - 5833 - - - ENA Sample Accession Number - ERS042051 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - 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Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5056.xml b/t/data/npg_api/st/samples/5056.xml deleted file mode 100644 index 90b4985d..00000000 --- a/t/data/npg_api/st/samples/5056.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5056 - DE303 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - DE303 - - - Common Name - Shigella sonnei - - - Strain - DE303 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008111 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5057.xml b/t/data/npg_api/st/samples/5057.xml deleted file mode 100644 index 02403614..00000000 --- a/t/data/npg_api/st/samples/5057.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5057 - DE199 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - DE199 - - - Common Name - Shigella sonnei - - - Strain - DE199 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008112 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5058.xml b/t/data/npg_api/st/samples/5058.xml deleted file mode 100644 index f5a700bc..00000000 --- a/t/data/npg_api/st/samples/5058.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5058 - DE1191 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - DE1191 - - - Common Name - Shigella sonnei - - - Strain - DE1191 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008113 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5059.xml b/t/data/npg_api/st/samples/5059.xml deleted file mode 100644 index a8210116..00000000 --- a/t/data/npg_api/st/samples/5059.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5059 - DE1336 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - DE1336 - - - Common Name - Shigella sonnei - - - Strain - DE1336 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008114 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5060.xml b/t/data/npg_api/st/samples/5060.xml deleted file mode 100644 index ed263c2a..00000000 --- a/t/data/npg_api/st/samples/5060.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5060 - EG467 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - EG467 - - - Common Name - Shigella sonnei - - - Strain - EG467 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008115 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5061.xml b/t/data/npg_api/st/samples/5061.xml deleted file mode 100644 index 0c37bccb..00000000 --- a/t/data/npg_api/st/samples/5061.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5061 - EG304 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - EG304 - - - Common Name - Shigella sonnei - - - Strain - EG304 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008116 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5062.xml b/t/data/npg_api/st/samples/5062.xml deleted file mode 100644 index 12457bb2..00000000 --- a/t/data/npg_api/st/samples/5062.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5062 - EG472 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - EG472 - - - Common Name - Shigella sonnei - - - Strain - EG472 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008117 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/samples/5063.xml b/t/data/npg_api/st/samples/5063.xml deleted file mode 100644 index 2194e437..00000000 --- a/t/data/npg_api/st/samples/5063.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5063 - EG365 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - - - - Public Name - EG365 - - - Common Name - Shigella sonnei - - - Strain - EG365 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS008118 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - 297 - diff --git a/t/data/npg_api/st/studies/297.xml b/t/data/npg_api/st/studies/297.xml deleted file mode 100644 index 34ccaa7b..00000000 --- a/t/data/npg_api/st/studies/297.xml +++ /dev/null @@ -1,193 +0,0 @@ - - - 297 - Discovery of sequence diversity in Shigella sp. - true - 206 - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - tc7 - tc7@sanger.ac.uk - Thomas Connor - 475 - - - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - jm15 - jm15@sanger.ac.uk - Jacqueline McQuillan - 67 - - - nds - nds@sanger.ac.uk - Nishadi De Silva - 383 - - - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - - - 2009-04-27 11:46:48 +0100 - 2010-09-09 14:27:54 +0100 - - - Has this been approved? - - - - Delay for - - - - Study description - For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/shigella-sonnei.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - ENA Study Accession Number - ERP000182 - - - Title - Discovery of sequence diversity in Shigella sp. - - - SNP study ID - - - - Abstract - For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/shigella-sonnei.html - - - Study name abbreviation - - - - Do any of the samples in this study contain human DNA? - No - - - Study Visibility - Hold - - - Has the delay period been approved by the data sharing committee for this project? - - - - ArrayExpress Accession Number - - - - How is the data release to be timed? - standard - - - SNP parent study ID - - - - EGA DAC Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - What is the data release strategy for this study? - open - - - EGA Policy Accession Number - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Reason for delaying release - - - - Policy - - - - ENA Project ID - - - - Comment regarding prevention of data release and approval - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Comment regarding data release timing and approval - - - - Alignments in BAM - true - - - Will you be using WTSI's standard access agreement? - - - - Faculty Sponsor - Julian Parkhill - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Study Type - Whole Genome Sequencing - - - diff --git a/t/data/npg_api/st/studies/546.xml b/t/data/npg_api/st/studies/546.xml deleted file mode 100644 index d2b04efe..00000000 --- a/t/data/npg_api/st/studies/546.xml +++ /dev/null @@ -1,199 +0,0 @@ - - - 546 - Plasmodium falciparum Illumina sequencing R&D 1 - true - 29 - - - vrr - vrr@sanger.ac.uk - Valentin Ruano Rubio - 282 - - - glm - glm@sanger.ac.uk - Gareth Maslen - 34 - - - sc11 - sc11@sanger.ac.uk - Susana Campino - 114 - - - so1 - so1@sanger.ac.uk - Samuel Oyola - 419 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - da2 - da2@sanger.ac.uk - Daniel Alcock - 335 - - - ekh - ekh@sanger.ac.uk - Eleanor Howard - 128 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - 2010-04-25 14:45:24 +0100 - 2010-04-26 12:09:41 +0100 - - - Has this been approved? - - - - Delay for - - - - Study description - To develop and improve methods for Illumina sequencing of Plasmodium faliciparum clinical samples. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - ENA Study Accession Number - ERP000197 - - - Title - Plasmodium falciparum Illumina sequencing R&D - - - SNP study ID - - - - Abstract - Development and optimization of pre-sequencing sample preparation methods with the goal of improving data yield and quality while reducing costs of sequencing per sample - - - Study name abbreviation - - - - Do any of the samples in this study contain human DNA? - Yes - - - Study Visibility - Hold - - - Has the delay period been approved by the data sharing committee for this project? - - - - ArrayExpress Accession Number - - - - How is the data release to be timed? - standard - - - SNP parent study ID - - - - EGA DAC Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - What is the data release strategy for this study? - open - - - EGA Policy Accession Number - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - Yes - - - Reason for delaying release - - - - Policy - - - - ENA Project ID - 0 - - - Comment regarding prevention of data release and approval - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Comment regarding data release timing and approval - - - - Alignments in BAM - true - - - Will you be using WTSI's standard access agreement? - - - - Faculty Sponsor - Dominic Kwiatkowski - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Study Type - Whole Genome Sequencing - - - diff --git a/t/data/npg_api/st/studies/578.xml b/t/data/npg_api/st/studies/578.xml deleted file mode 100644 index 30462a1e..00000000 --- a/t/data/npg_api/st/studies/578.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - 578 - Plasmodium falciparum genome variation 1 - true - 29 - - - sc11 - sc11@sanger.ac.uk - Susana Campino - 114 - - - vrr - vrr@sanger.ac.uk - Valentin Ruano Rubio - 282 - - - glm - glm@sanger.ac.uk - Gareth Maslen - 34 - - - mm6 - mm6@sanger.ac.uk - Magnus Manske - 99 - - - ekh - ekh@sanger.ac.uk - Eleanor Howard - 128 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - da2 - da2@sanger.ac.uk - Daniel Alcock - 335 - - - ekh - ekh@sanger.ac.uk - Eleanor Howard - 128 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - 2010-05-17 15:28:19 +0100 - 2010-05-24 16:39:52 +0100 - - - Has this been approved? - - - - Delay for - - - - Study description - Genome sequencing of field samples of Plasmodium falciparum. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - ENA Study Accession Number - ERP000190 - - - Title - Plasmodium falciparum natural genome variation - - - SNP study ID - - - - Abstract - Direct or cultured field isolates of Plasmodium falciparum are being sequenced to provide contributing investigators with genetic data to support locally-driven studies, while also contributing to the development of a repository of natural P. falciparum genome variation. This global dataset will provide a resource for genome-wide association studies and other genomic studies aimed at identifying genetic loci responsible for such phenotypes as antimalarial drug resistance. For information on the Plasmodium genome variation project, contributing investigators and studies, sample details, and data sharing policies please visit http://www.malariagen.net/projects/parasite - - - Study name abbreviation - - - - Do any of the samples in this study contain human DNA? - Yes - - - Study Visibility - Hold - - - Has the delay period been approved by the data sharing committee for this project? - - - - ArrayExpress Accession Number - - - - How is the data release to be timed? - standard - - - SNP parent study ID - - - - EGA DAC Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - What is the data release strategy for this study? - open - - - EGA Policy Accession Number - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - Yes - - - Reason for delaying release - - - - Policy - - - - ENA Project ID - 0 - - - Comment regarding prevention of data release and approval - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Comment regarding data release timing and approval - - - - Alignments in BAM - true - - - Will you be using WTSI's standard access agreement? - - - - Faculty Sponsor - Dominic Kwiatkowski - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Study Type - Whole Genome Sequencing - - - diff --git a/t/data/npg_api_run/npg/run/604.xml b/t/data/npg_api_run/npg/run/604.xml deleted file mode 100644 index 84e18108..00000000 --- a/t/data/npg_api_run/npg/run/604.xml +++ /dev/null @@ -1,52 +0,0 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/npg_api_run/npg/run/636.xml b/t/data/npg_api_run/npg/run/636.xml deleted file mode 100644 index 87b3aef1..00000000 --- a/t/data/npg_api_run/npg/run/636.xml +++ /dev/null @@ -1,34 +0,0 @@ - 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- - - - - - - - - - 2072 - diff --git a/t/data/repos1/st/samples/1382839.xml b/t/data/repos1/st/samples/1382839.xml deleted file mode 100644 index 48ce38bd..00000000 --- a/t/data/repos1/st/samples/1382839.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1382839 - HALO_GV1 - 1980 - false - - - Organism - - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - - - - Common Name - - - - Strain - - - - TAXON ID - - - - ENA Sample Accession Number - - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - 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Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001188802 - - - Sample Description - Total RNA from iPS-derived macrophages using mirVana - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - Normal - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - iPS-derived macrophage - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - control - - - Subject - - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38 + ensembl_75_transcriptome) - - - - - - - - - - 2899 - diff --git a/t/data/repos1/st/samples/1830658.xml b/t/data/repos1/st/samples/1830658.xml deleted file mode 100644 index 5278bc22..00000000 --- a/t/data/repos1/st/samples/1830658.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1830658 - FSPS_10c_ctrl - 2910 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - FSPS_10c_ctrl - - - DNA source - Genomic - - - Public Name - FSPS 10c ctrl - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001188802 - - - Sample Description - Total RNA from iPS-derived macrophages using mirVana - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - Normal - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - iPS-derived macrophage - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - control - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - 2910 - diff --git a/t/data/repos1/st/studies/2072.xml b/t/data/repos1/st/studies/2072.xml deleted file mode 100644 index 10240d80..00000000 --- a/t/data/repos1/st/studies/2072.xml +++ /dev/null @@ -1,179 +0,0 @@ - - - 2072 - SEQCAP_Dyslipidemia_families_FY2011_12 - true - 137 - - - eh4 - eh4@sanger.ac.uk - Eija Hamalainen - 337 - - - - - dw2 - dw2@sanger.ac.uk - Danielle Walker - 86 - - - - - dw2 - dw2@sanger.ac.uk - Danielle Walker - 86 - - - - - 2011-12-19 13:19:12 +0000 - 2012-11-26 14:20:21 +0000 - - - Study description - These samples include exome sequences of family members with dyslipidemias from Finnish origin. - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - ENA Project ID - - - - Abstract - These samples include exome sequences of family members with dyslipidemias from Finnish origin. - - - Title - Dyslipidemia - - - ENA Study Accession Number - EGAS00001000189 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - SC_DYSLIPFAM - - - What is the data release strategy for this study? - managed - - - Will you be using WTSI's standard access agreement? - Yes - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Comment regarding data release timing and approval - - - - Policy - The data will be submitted to EGA and are accessible under managed data access. -https://www.sanger.ac.uk/datasharing/ - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - 7.0 - - - HMDMC approval number - - - - Study Type - Exome Sequencing - - - What sort of study is this? - genomic sequencing - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - Faculty Sponsor - Aarno Palotie - - - diff --git a/t/data/repos1/st/studies/2910.xml b/t/data/repos1/st/studies/2910.xml deleted file mode 100644 index f807dbc4..00000000 --- a/t/data/repos1/st/studies/2910.xml +++ /dev/null @@ -1,196 +0,0 @@ - - - 2910 - I1548 - miRNA expression in response to LPS stimulus in macrophages - true - 191 - - - ncb - ncb@sanger.ac.uk - Nathalie C Smerdon - 191 - - - jb4 - jb4@sanger.ac.uk - Jacqueline Brown - 351 - - - - - dg13 - dg13@sanger.ac.uk - Daniel Gaffney - 545 - - - - - 2014-01-14 10:49:48 +0000 - 2014-02-12 09:04:05 +0000 - - - Study description - Our lab is currently using macrophages as a model system for understanding how genetic -variation modulates the response to external environmental stimulus. We want to extend this -beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would -cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as -part of a rotation project in the lab. We will require a small number of miRNA libraries and a -single lane of MiSeq - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - - - - Abstract - Our lab is currently using macrophages as a model system for understanding how genetic -variation modulates the response to external environmental stimulus. We want to extend this -beyond regular polyadenylated RNA to small RNAs such as miRNAs. This project would -cover the costs of a pilot to study miRNA response to LPS stimulus, and will be performed as -part of a rotation project in the lab. We will require a small number of miRNA libraries and a single lane of MiSeq - - - Title - miRNA expression in response to LPS stimulus in macrophages - - - ENA Study Accession Number - EGAS00001000691 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - macrophage_miRNA - - - What is the data release strategy for this study? - managed - - - Will you be using WTSI's standard access agreement? - Yes - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - http://www.sanger.ac.uk/datasharing/ - - - Policy title - Wellcome Trust Sanger Institute Data Sharing Policy - - - EGA DAC Accession Number - 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Forward run ID - 261 - - - reverse_run_id - Reverse run ID - 276 - - - forward_yield - Forward yield - 206758939 - - - reverse_yield - Reverse yield - 194283734 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5522 - - - forward_run_id - Forward run ID - 261 - - - reverse_run_id - Reverse run ID - 276 - - - forward_yield - Forward yield - 205919272 - - - reverse_yield - Reverse yield - 193398341 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5523 - - - forward_run_id - Forward run ID - 261 - - - reverse_run_id - Reverse run ID - 276 - - - forward_yield - Forward yield - 204331952 - - - reverse_yield - Reverse yield - 192072244 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5524 - - - forward_run_id - Forward run ID - 261 - - - reverse_run_id - Reverse run ID - 276 - - - forward_yield - Forward yield - 213047920 - - - reverse_yield - Reverse yield - 200149539 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5525 - - - forward_run_id - Forward run ID - 261 - - - reverse_run_id - Reverse run ID - 276 - - - forward_yield - Forward yield - 210365260 - - - reverse_yield - Reverse yield - 197633828 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5526 - - - forward_run_id - Forward run ID - 261 - - - reverse_run_id - Reverse run ID - 276 - - - forward_yield - Forward yield - 197148495 - - - reverse_yield - Reverse yield - 185309346 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5527 - - - forward_run_id - Forward run ID - 321 - - - reverse_run_id - Reverse run ID - 346 - - - forward_yield - Forward yield - 175206083 - - - reverse_yield - Reverse yield - 162038835 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5528 - - - forward_run_id - Forward run ID - 321 - - - reverse_run_id - Reverse run ID - 346 - - - forward_yield - Forward yield - 191105425 - - - reverse_yield - Reverse yield - 169088613 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5529 - - - forward_run_id - Forward run ID - 321 - - - reverse_run_id - Reverse run ID - 346 - - - forward_yield - Forward yield - 190257931 - - - reverse_yield - Reverse yield - 162851942 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5530 - - - forward_run_id - Forward run ID - 321 - - - reverse_run_id - Reverse run ID - 346 - - - forward_yield - Forward yield - 188006995 - - - reverse_yield - Reverse yield - 157726099 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5531 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 197907760 - - - reverse_yield - Reverse yield - 191562981 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5532 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 212026413 - - - reverse_yield - Reverse yield - 206066984 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5533 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 214966437 - - - reverse_yield - Reverse yield - 204553348 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5534 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 210281684 - - - reverse_yield - Reverse yield - 202996551 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5535 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 210941855 - - - reverse_yield - Reverse yield - 203894004 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5536 - - - forward_run_id - Forward run ID - 323 - - - reverse_run_id - Reverse run ID - 341 - - - forward_yield - Forward yield - 217111233 - - - reverse_yield - Reverse yield - 202381996 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5537 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 204962236 - - - reverse_yield - Reverse yield - 195357280 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5538 - - - forward_run_id - Forward run ID - 323 - - - reverse_run_id - Reverse run ID - 341 - - - forward_yield - Forward yield - 224955806 - - - reverse_yield - Reverse yield - 210515233 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5539 - - - forward_run_id - Forward run ID - 240 - - - reverse_run_id - Reverse run ID - 253 - - - forward_yield - Forward yield - 204078303 - - - reverse_yield - Reverse yield - 194013295 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5540 - - - forward_run_id - Forward run ID - 323 - - - reverse_run_id - Reverse run ID - 341 - - - forward_yield - Forward yield - 226665926 - - - reverse_yield - Reverse yield - 212089575 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5541 - - - forward_run_id - Forward run ID - 323 - - - reverse_run_id - Reverse run ID - 341 - - - forward_yield - Forward yield - 222688280 - - - reverse_yield - Reverse yield - 208585107 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5542 - - - forward_run_id - Forward run ID - 323 - - - reverse_run_id - Reverse run ID - 341 - - - forward_yield - Forward yield - 222055904 - - - reverse_yield - Reverse yield - 207875649 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5543 - - - forward_run_id - Forward run ID - 309 - - - forward_run_id - Forward run ID - 323 - - - reverse_run_id - Reverse run ID - 341 - - - forward_yield - Forward yield - 209443991 - - - reverse_yield - Reverse yield - 195733029 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5544 - - - forward_run_id - Forward run ID - 309 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 201681352 - - - reverse_yield - Reverse yield - 190916588 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5545 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 179612323 - - - reverse_yield - Reverse yield - 170783934 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5546 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 184633707 - - - reverse_yield - Reverse yield - 175460309 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 5547 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 184734945 - - - reverse_yield - Reverse yield - 175362068 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10890 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 193627713 - - - reverse_yield - Reverse yield - 183981689 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10891 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 191407361 - - - reverse_yield - Reverse yield - 182029999 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10892 - - - forward_run_id - Forward run ID - 278 - - - reverse_run_id - Reverse run ID - 309 - - - forward_yield - Forward yield - 177519831 - - - reverse_yield - Reverse yield - 168979441 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10893 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 123349316 - - - reverse_yield - Reverse yield - 114808066 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10894 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 114880602 - - - reverse_yield - Reverse yield - 107994629 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10895 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 147290030 - - - reverse_yield - Reverse yield - 140875973 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10896 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 122020422 - - - reverse_yield - Reverse yield - 114514685 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10897 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 124735077 - - - reverse_yield - Reverse yield - 118335235 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10898 - - - forward_run_id - Forward run ID - 311 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 126665986 - - - reverse_yield - Reverse yield - 120664661 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10899 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 125761308 - - - reverse_yield - Reverse yield - 119767621 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10900 - - - forward_run_id - Forward run ID - 246 - - - reverse_run_id - Reverse run ID - 260 - - - forward_yield - Forward yield - 122400218 - - - reverse_yield - Reverse yield - 116335452 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10901 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 210456484 - - - reverse_yield - Reverse yield - 182095987 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10902 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 216061433 - - - reverse_yield - Reverse yield - 185684628 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10903 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 144454331 - - - reverse_yield - Reverse yield - 139639087 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10904 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 143387352 - - - reverse_yield - Reverse yield - 139181328 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10905 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 215723783 - - - reverse_yield - Reverse yield - 183045456 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10906 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 144569333 - - - reverse_yield - Reverse yield - 140215493 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10907 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 220153095 - - - reverse_yield - Reverse yield - 185869282 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10908 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 144198016 - - - reverse_yield - Reverse yield - 139859064 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10909 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 142097605 - - - reverse_yield - Reverse yield - 137454293 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10910 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 218039906 - - - reverse_yield - Reverse yield - 184746182 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10911 - - - forward_run_id - Forward run ID - 279 - - - reverse_run_id - Reverse run ID - 311 - - - forward_yield - Forward yield - 142786451 - - - reverse_yield - Reverse yield - 138957871 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10912 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 214892800 - - - reverse_yield - Reverse yield - 180279553 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10913 - - - forward_run_id - Forward run ID - 248 - - - reverse_run_id - Reverse run ID - 256 - - - forward_yield - Forward yield - 203402408 - - - reverse_yield - Reverse yield - 171143400 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10914 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 162432757 - - - reverse_yield - Reverse yield - 147761097 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10915 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 162142678 - - - reverse_yield - Reverse yield - 147394140 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10916 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 161179968 - - - reverse_yield - Reverse yield - 139052817 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10917 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 167499380 - - - reverse_yield - Reverse yield - 150653529 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10918 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 185121043 - - - reverse_yield - Reverse yield - 168935944 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10919 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 181066827 - - - reverse_yield - Reverse yield - 166300189 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10920 - - - forward_run_id - Forward run ID - 249 - - - reverse_run_id - Reverse run ID - 262 - - - forward_yield - Forward yield - 178967927 - - - reverse_yield - Reverse yield - 164141061 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10921 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 196924961 - - - reverse_yield - Reverse yield - 175090133 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10922 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 210201860 - - - reverse_yield - Reverse yield - 190233274 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10923 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 195791394 - - - reverse_yield - Reverse yield - 178472701 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10924 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 200798194 - - - reverse_yield - Reverse yield - 183179044 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10925 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 221620601 - - - reverse_yield - Reverse yield - 201849310 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10926 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 222855809 - - - reverse_yield - Reverse yield - 203815959 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10927 - - - forward_run_id - Forward run ID - 289 - - - reverse_run_id - Reverse run ID - 301 - - - forward_yield - Forward yield - 214699757 - - - reverse_yield - Reverse yield - 194903459 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10928 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 188579613 - - - reverse_yield - Reverse yield - 174585196 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10929 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 194194643 - - - reverse_yield - Reverse yield - 179279018 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10930 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 202547928 - - - reverse_yield - Reverse yield - 188668335 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10931 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 200565320 - - - reverse_yield - Reverse yield - 186750399 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10932 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 200660983 - - - reverse_yield - Reverse yield - 187135108 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10933 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 198368315 - - - reverse_yield - Reverse yield - 184941776 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10934 - - - forward_run_id - Forward run ID - 291 - - - reverse_run_id - Reverse run ID - 302 - - - forward_yield - Forward yield - 194512413 - - - reverse_yield - Reverse yield - 181125700 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10935 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 188875195 - - - reverse_yield - Reverse yield - 177780885 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10936 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 199179336 - - - reverse_yield - Reverse yield - 187209445 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10937 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 196157214 - - - reverse_yield - Reverse yield - 184337080 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10938 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 202412587 - - - reverse_yield - Reverse yield - 190864871 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10939 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 200097885 - - - reverse_yield - Reverse yield - 189135903 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10940 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 197156968 - - - reverse_yield - Reverse yield - 186376349 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10941 - - - forward_run_id - Forward run ID - 296 - - - reverse_run_id - Reverse run ID - 320 - - - forward_yield - Forward yield - 195400948 - - - reverse_yield - Reverse yield - 184789233 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10942 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 80911246 - - - reverse_yield - Reverse yield - 58541946 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10943 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 87977907 - - - reverse_yield - Reverse yield - 64769806 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10944 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 91150582 - - - reverse_yield - Reverse yield - 67735991 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10945 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 90522341 - - - reverse_yield - Reverse yield - 67055748 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10946 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 87406545 - - - reverse_yield - Reverse yield - 65123260 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10947 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 79072569 - - - reverse_yield - Reverse yield - 58454282 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10948 - - - forward_run_id - Forward run ID - 138 - - - reverse_run_id - Reverse run ID - 142 - - - forward_yield - Forward yield - 71057839 - - - reverse_yield - Reverse yield - 51946650 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10949 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 182889214 - - - reverse_yield - Reverse yield - 151079677 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10950 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 196675240 - - - reverse_yield - Reverse yield - 163677170 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10951 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 196371980 - - - reverse_yield - Reverse yield - 165294758 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10952 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 193845896 - - - reverse_yield - Reverse yield - 164972888 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10953 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 196740691 - - - reverse_yield - Reverse yield - 166163749 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10954 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 189915345 - - - reverse_yield - Reverse yield - 159329598 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10955 - - - forward_run_id - Forward run ID - 141 - - - reverse_run_id - Reverse run ID - 152 - - - forward_yield - Forward yield - 185626801 - - - reverse_yield - Reverse yield - 155898377 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10956 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 67713374 - - - reverse_yield - Reverse yield - 26838532 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10957 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 91295107 - - - reverse_yield - Reverse yield - 53126471 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10958 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 77713603 - - - reverse_yield - Reverse yield - 42421336 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10959 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 109281067 - - - reverse_yield - Reverse yield - 59430423 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10960 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 104787862 - - - reverse_yield - Reverse yield - 52457465 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10961 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 114686150 - - - reverse_yield - Reverse yield - 66466573 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10962 - - - forward_run_id - Forward run ID - 144 - - - reverse_run_id - Reverse run ID - 153 - - - forward_yield - Forward yield - 112000705 - - - reverse_yield - Reverse yield - 65140631 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10963 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 124898976 - - - reverse_yield - Reverse yield - 91244598 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10964 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 120392892 - - - reverse_yield - Reverse yield - 85917143 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10965 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 111179550 - - - reverse_yield - Reverse yield - 77112075 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10966 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 129223920 - - - reverse_yield - Reverse yield - 94359324 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10967 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 126715456 - - - reverse_yield - Reverse yield - 94266468 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10968 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 129031786 - - - reverse_yield - Reverse yield - 94515369 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10969 - - - forward_run_id - Forward run ID - 145 - - - reverse_run_id - Reverse run ID - 154 - - - forward_yield - Forward yield - 118521562 - - - reverse_yield - Reverse yield - 87150307 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10970 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 106598986 - - - reverse_yield - Reverse yield - 102776326 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10971 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 98473204 - - - reverse_yield - Reverse yield - 94339936 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10972 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 77790986 - - - reverse_yield - Reverse yield - 72947338 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10973 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 106766148 - - - reverse_yield - Reverse yield - 104582053 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10974 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 99248316 - - - reverse_yield - Reverse yield - 95867237 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10975 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 110372904 - - - reverse_yield - Reverse yield - 109135723 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10976 - - - forward_run_id - Forward run ID - 157 - - - reverse_run_id - Reverse run ID - 168 - - - forward_yield - Forward yield - 106418374 - - - reverse_yield - Reverse yield - 104772779 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10977 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 109265259 - - - reverse_yield - Reverse yield - 96026887 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10978 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 103854760 - - - reverse_yield - Reverse yield - 90977354 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10979 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 97557361 - - - reverse_yield - Reverse yield - 82851246 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10980 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 110306855 - - - reverse_yield - Reverse yield - 97564081 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10981 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 106895194 - - - reverse_yield - Reverse yield - 93788477 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10982 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 111620732 - - - reverse_yield - Reverse yield - 99483308 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10983 - - - forward_run_id - Forward run ID - 158 - - - reverse_run_id - Reverse run ID - 170 - - - forward_yield - Forward yield - 59200430 - - - reverse_yield - Reverse yield - 50255914 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10984 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 108131196 - - - reverse_yield - Reverse yield - 85744740 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10985 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 99781776 - - - reverse_yield - Reverse yield - 81378806 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10986 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 92965509 - - - reverse_yield - Reverse yield - 76193839 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10987 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 106499918 - - - reverse_yield - Reverse yield - 84195212 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10988 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 103233989 - - - reverse_yield - Reverse yield - 83848149 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10989 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 102658233 - - - reverse_yield - Reverse yield - 80980032 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10990 - - - forward_run_id - Forward run ID - 159 - - - reverse_run_id - Reverse run ID - 169 - - - forward_yield - Forward yield - 94051951 - - - reverse_yield - Reverse yield - 73431532 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10991 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 88755445 - - - reverse_yield - Reverse yield - 74698496 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10992 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 80807028 - - - reverse_yield - Reverse yield - 70311759 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10993 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 57494060 - - - reverse_yield - Reverse yield - 48548915 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10994 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 87450365 - - - reverse_yield - Reverse yield - 75819818 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10995 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 71384113 - - - reverse_yield - Reverse yield - 61544796 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10996 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 86843495 - - - reverse_yield - Reverse yield - 74448969 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10997 - - - forward_run_id - Forward run ID - 166 - - - reverse_run_id - Reverse run ID - 171 - - - forward_yield - Forward yield - 80746420 - - - reverse_yield - Reverse yield - 69752074 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10998 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 171227645 - - - reverse_yield - Reverse yield - 151511221 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 10999 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 154857494 - - - reverse_yield - Reverse yield - 129844791 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11000 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 176490991 - - - reverse_yield - Reverse yield - 157671082 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11001 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 183253510 - - - reverse_yield - Reverse yield - 161635843 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11002 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 179726054 - - - reverse_yield - Reverse yield - 158205545 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11003 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 180977210 - - - reverse_yield - Reverse yield - 161096076 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11004 - - - forward_run_id - Forward run ID - 180 - - - reverse_run_id - Reverse run ID - 182 - - - forward_yield - Forward yield - 172577633 - - - reverse_yield - Reverse yield - 152801754 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11005 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 172061038 - - - reverse_yield - Reverse yield - 123546779 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11006 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 154919960 - - - reverse_yield - Reverse yield - 108033975 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11007 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 180683087 - - - reverse_yield - Reverse yield - 130040296 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11008 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 181377246 - - - reverse_yield - Reverse yield - 125511098 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11009 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 178172861 - - - reverse_yield - Reverse yield - 126027873 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11010 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 185142395 - - - reverse_yield - Reverse yield - 132583384 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11011 - - - forward_run_id - Forward run ID - 181 - - - reverse_run_id - Reverse run ID - 183 - - - forward_yield - Forward yield - 175830211 - - - reverse_yield - Reverse yield - 126462913 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11012 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 188905492 - - - reverse_yield - Reverse yield - 181156398 - - - lane - Lane - 1 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11013 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 208324547 - - - reverse_yield - Reverse yield - 198865030 - - - lane - Lane - 2 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11014 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 206786347 - - - reverse_yield - Reverse yield - 198596298 - - - lane - Lane - 3 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11015 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 200649775 - - - reverse_yield - Reverse yield - 193064296 - - - lane - Lane - 5 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11016 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 220603969 - - - reverse_yield - Reverse yield - 211315457 - - - lane - Lane - 6 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11017 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 200912558 - - - reverse_yield - Reverse yield - 193230798 - - - lane - Lane - 7 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 11018 - - - forward_run_id - Forward run ID - 193 - - - reverse_run_id - Reverse run ID - 208 - - - forward_yield - Forward yield - 195706380 - - - reverse_yield - Reverse yield - 188856455 - - - lane - Lane - 8 - - - read_length - Read length - 37 - - - fragment_size_required_from - Fragment size required (from) - 200 - - - fragment_size_required_to - Fragment size required (to) - - - - - - 43998 - - - - - 43999 - - - - - 44000 - - - - - 44001 - - - - - 44022 - - - - - 44023 - - - - - 44024 - - - - - 44025 - - - - - 44026 - - - - - 44027 - - - - - 44028 - - - - - 44029 - - - - - 44030 - - - - - 44031 - - - - - 44032 - - - - - diff --git a/t/data/st_api_lims_new/st/assets/3033734.xml b/t/data/st_api_lims_new/st/assets/3033734.xml deleted file mode 100644 index 2a846202..00000000 --- a/t/data/st_api_lims_new/st/assets/3033734.xml +++ /dev/null @@ -1,81 +0,0 @@ - - - 3033734 - LibraryTube - BS_3hrsomuleSm_202790 3033734 - - pending - 1121926 - - - - - 3213730 - 3323725 - - - 3145063 - - - - 3156170 - - - fragment_size_required_from - Fragment size required (from) - 150 - - - read_length - Read length - 75 - - - fragment_size_required_to - Fragment size required (to) - 500 - - - - - 3456759 - - - fragment_size_required_from - Fragment size required (from) - 150 - - - read_length - Read length - 75 - - - fragment_size_required_to - Fragment size required (to) - 500 - - - - - 3456767 - - - fragment_size_required_from - Fragment size required (from) - 150 - - - read_length - Read length - 75 - - - fragment_size_required_to - Fragment size required (to) - 500 - - - - - diff --git a/t/data/st_api_lims_new/st/assets/3111688.xml b/t/data/st_api_lims_new/st/assets/3111688.xml deleted file mode 100644 index be2a9d96..00000000 --- a/t/data/st_api_lims_new/st/assets/3111688.xml +++ /dev/null @@ -1,157 +0,0 @@ - - - 3111688 - MultiplexedLibraryTube - 3C_HiC_Pool3 - - pending - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - 3213734 - 3323727 - - - 3111679 - 3111680 - 3111681 - 3111682 - 3111683 - 3111684 - 3111685 - 3111686 - 3111687 - - - - 3259935 - - - fragment_size_required_from - Fragment size required (from) - 400 - - - read_length - Read length - 75 - - - fragment_size_required_to - Fragment size required (to) - 600 - - - - - 3456761 - - - fragment_size_required_from - Fragment size required (from) - 400 - - - read_length - Read length - 75 - - - fragment_size_required_to - Fragment size required (to) - 600 - - - - - 3456769 - - - fragment_size_required_from - Fragment size required (from) - 400 - - - read_length - Read length - 75 - - - fragment_size_required_to - Fragment size required (to) - 600 - - - - - diff --git a/t/data/st_api_lims_new/st/batches/12141.xml b/t/data/st_api_lims_new/st/batches/12141.xml deleted file mode 100644 index ae4023ea..00000000 --- a/t/data/st_api_lims_new/st/batches/12141.xml +++ /dev/null @@ -1,1463 +0,0 @@ - - - 12141 - released - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - 23 - TGCATAGTAT - 7 - - - - - - 24 - TTGACTCTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - 23 - TGCATAGTAT - 7 - - - - - - 24 - TTGACTCTAT - 7 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - diff --git a/t/data/st_api_lims_new/st/batches/12378.xml b/t/data/st_api_lims_new/st/batches/12378.xml deleted file mode 100644 index a4d3fb39..00000000 --- a/t/data/st_api_lims_new/st/batches/12378.xml +++ /dev/null @@ -1,443 +0,0 @@ - - - 12378 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - 4 - TGACCACTAT - 7 - - - - - - 5 - ACAGTGGTAT - 7 - - - - - - 6 - GCCAATGTAT - 7 - - - - - - 7 - CAGATCTGAT - 7 - - - - - - 8 - ACTTGATGAT - 7 - - - - - - 9 - GATCAGCGAT - 7 - - - - - - 10 - TAGCTTGTAT - 7 - - - - - - 11 - GGCTACAGAT - 7 - - - - - - 12 - CTTGTACTAT - 7 - - - - - - 13 - TGGTTGTTAT - 7 - - - - - - 14 - TCTCGGTTAT - 7 - - - - - - 15 - TAAGCGTTAT - 7 - - - - - - 16 - TCCGTCTTAT - 7 - - - - - - 17 - TGTACCTTAT - 7 - - - - - - 18 - TTCTGTGTAT - 7 - - - - - - 19 - TCTGCTGTAT - 7 - - - - - - 20 - TTGGAGGTAT - 7 - - - - - - 21 - TCGAGCGTAT - 7 - - - - - - 22 - TGATACGTAT - 7 - - - - - - 23 - TGCATAGTAT - 7 - - - - - - 24 - TTGACTCTAT - 7 - - - - - - - - - - 1 - ATCACGTTAT - 4 - - - - - - 2 - CGATGTTTAT - 4 - - - - - - 3 - TTAGGCATAT - 4 - - - - - - 4 - TGACCACTAT - 4 - - - - - - 5 - ACAGTGGTAT - 4 - - - - - - 6 - GCCAATGTAT - 4 - - - - - - 7 - CAGATCTGAT - 4 - - - - - - 8 - ACTTGATGAT - 4 - - - - - - 9 - GATCAGCGAT - 4 - - - - - - 10 - TAGCTTGTAT - 4 - - - - - - 11 - GGCTACAGAT - 4 - - - - - - 12 - CTTGTACTAT - 4 - - - - - - - - - - 1 - ATCACGTTAT - 4 - - - - - - 2 - CGATGTTTAT - 4 - - - - - - 3 - TTAGGCATAT - 4 - - - - - - 4 - TGACCACTAT - 4 - - - - - - - diff --git a/t/data/st_api_lims_new/st/batches/13410.xml b/t/data/st_api_lims_new/st/batches/13410.xml deleted file mode 100644 index 5e464241..00000000 --- a/t/data/st_api_lims_new/st/batches/13410.xml +++ /dev/null @@ -1,527 +0,0 @@ - - - 13410 - released - - - - - - 2 - CGATGT - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - diff --git a/t/data/st_api_lims_new/st/batches/17763.xml b/t/data/st_api_lims_new/st/batches/17763.xml deleted file mode 100644 index 4f688ef4..00000000 --- a/t/data/st_api_lims_new/st/batches/17763.xml +++ /dev/null @@ -1,944 +0,0 @@ - - - 17763 - released - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 33 - TCGAAGTG - 6 - - - - - - 34 - TAACGCTG - 6 - - - - - - 35 - TTGGTATG - 6 - - - - - - 36 - TGAACTGG - 6 - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 33 - TCGAAGTG - 6 - - - - - - 34 - TAACGCTG - 6 - - - - - - 35 - TTGGTATG - 6 - - - - - - 36 - TGAACTGG - 6 - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - 16 - TCCGTCTT - 6 - - - - - - 17 - TGTACCTT - 6 - - - - - - 18 - TTCTGTGT - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 19 - TCTGCTGT - 6 - - - - - - 20 - TTGGAGGT - 6 - - - - - - 21 - TCGAGCGT - 6 - - - - - - 22 - TGATACGT - 6 - - - - - - 23 - TGCATAGT - 6 - - - - - - 24 - TTGACTCT - 6 - - - - - - 25 - TGCGATCT - 6 - - - - - - 26 - TTCCTGCT - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - 16 - TCCGTCTT - 6 - - - - - - 17 - TGTACCTT - 6 - - - - - - 18 - TTCTGTGT - 6 - - - - - - 19 - TCTGCTGT - 6 - - - - - - 20 - TTGGAGGT - 6 - - - - - - 21 - TCGAGCGT - 6 - - - - - - 22 - TGATACGT - 6 - - - - - - 23 - TGCATAGT - 6 - - - - - - 24 - TTGACTCT - 6 - - - - - - 25 - TGCGATCT - 6 - - - - - - 26 - TTCCTGCT - 6 - - - - - - 27 - TAGTGACT - 6 - - - - - - 28 - TACAGGAT - 6 - - - - - - 29 - TCCTCAAT - 6 - - - - - - 30 - TGTGGTTG - 6 - - - - - - 31 - TAGTCTTG - 6 - - - - - - 32 - TTCCATTG - 6 - - - - - - 33 - TCGAAGTG - 6 - - - - - - 34 - TAACGCTG - 6 - - - - - - 35 - TTGGTATG - 6 - - - - - - 36 - TGAACTGG - 6 - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - 41 - TCCAGTCG - 6 - - - - - - 42 - TGTATGCG - 6 - - - - - - 43 - TCATTGAG - 6 - - - - - - 44 - TGGCTCAG - 6 - - - - - - 45 - TATGCCAG - 6 - - - - - - 46 - TCAGATTC - 6 - - - - - - 47 - TACTAGTC - 6 - - - - - - 48 - TTCAGCTC - 6 - - - - - - 49 - TGTCTATC - 6 - - - - - - 50 - TATGTGGC - 6 - - - - - - 51 - TTACTCGC - 6 - - - - - - 52 - TCGTTAGC - 6 - - - - - - 53 - TACCGAGC - 6 - - - - - - 54 - TGTTCTCC - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 55 - TTCGCACC - 6 - - - - - - 56 - TTGCGTAC - 6 - - - - - - 57 - TCTACGAC - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - diff --git a/t/data/st_api_lims_new/st/batches/22061.xml b/t/data/st_api_lims_new/st/batches/22061.xml deleted file mode 100644 index 078dda4e..00000000 --- a/t/data/st_api_lims_new/st/batches/22061.xml +++ /dev/null @@ -1,83 +0,0 @@ - - - 22061 - released - - - - - - 66 - TGAAGCCA - 6 - - - - - - 67 - TACCACCA - 6 - - - - - - 68 - TGCGTGAA - 6 - - - - - - 69 - GGTGAGTT - 6 - - - - - - 70 - GATCTCTT - 6 - - - - - - 71 - GTGTCCTT - 6 - - - - - - 72 - GACGGATT - 6 - - - - - - 73 - GCAACATT - 6 - - - - - - 74 - GGTCGTGT - 6 - - - - - - - diff --git a/t/data/st_api_lims_new/st/batches/22829.xml b/t/data/st_api_lims_new/st/batches/22829.xml deleted file mode 100644 index a057eb1b..00000000 --- a/t/data/st_api_lims_new/st/batches/22829.xml +++ /dev/null @@ -1,916 +0,0 @@ - - - 22829 - released - - - - - - 65 - TTGTTCCA - 6 - - - Human all exon V5 - - - - - - 66 - TGAAGCCA - 6 - - - Human all exon V5 - - - - - - 67 - TACCACCA - 6 - - - Human all exon V5 - - - - - - 68 - TGCGTGAA - 6 - - - Human all exon V5 - - - - - - 69 - GGTGAGTT - 6 - - - Human all exon V5 - - - - - - 70 - GATCTCTT - 6 - - - Human all exon V5 - - - - - - 71 - GTGTCCTT - 6 - - - Human all exon V5 - - - - - - 72 - GACGGATT - 6 - - - Human all exon V5 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 73 - GCAACATT - 6 - - - Human all exon V5 - - - - - - 74 - GGTCGTGT - 6 - - - Human all exon V5 - - - - - - 75 - GAATCTGT - 6 - - - Human all exon V5 - - - - - - 76 - GTACATCT - 6 - - - Human all exon V5 - - - - - - 77 - GAGGTGCT - 6 - - - Human all exon V5 - - - - - - 78 - GCATGGCT - 6 - - - Human all exon V5 - - - - - - 79 - GTTAGCCT - 6 - - - Human all exon V5 - - - - - - 80 - GTCGCTAT - 6 - - - Human all exon V5 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 81 - GGAATGAT - 6 - - - Human all exon V5 - - - - - - 82 - GAGCCAAT - 6 - - - Human all exon V5 - - - - - - 83 - GCTCCTTG - 6 - - - Human all exon V5 - - - - - - 84 - GTAAGGTG - 6 - - - Human all exon V5 - - - - - - 85 - GAGGATGG - 6 - - - Human all exon V5 - - - - - - 86 - GTTGTCGG - 6 - - - Human all exon V5 - - - - - - 87 - GGATTAGG - 6 - - - Human all exon V5 - - - - - - 88 - GATAGAGG - 6 - - - Human all exon V5 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 89 - GTGTGTCG - 6 - - - Human all exon V5 - - - - - - 90 - GCAATCCG - 6 - - - Human all exon V5 - - - - - - 91 - GACCTTAG - 6 - - - Human all exon V5 - - - - - - 92 - GCCTGTTC - 6 - - - Human all exon V5 - - - - - - 93 - GCACTGTC - 6 - - - Human all exon V5 - - - - - - 94 - GCTAACTC - 6 - - - Human all exon V5 - - - - - - 95 - GATTCATC - 6 - - - Human all exon V5 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 35 - - - - - - 2 - CGATGT - 35 - - - - - - 3 - TTAGGC - 35 - - - - - - 4 - TGACCA - 35 - - - - - - 5 - ACAGTG - 35 - - - - - - 6 - GCCAAT - 35 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - 16 - TCCGTCTT - 6 - - - - - - 17 - TGTACCTT - 6 - - - - - - 18 - TTCTGTGT - 6 - - - - - - 19 - TCTGCTGT - 6 - - - - - - 20 - TTGGAGGT - 6 - - - - - - 21 - TCGAGCGT - 6 - - - - - - 22 - TGATACGT - 6 - - - - - - 23 - TGCATAGT - 6 - - - - - - 24 - TTGACTCT - 6 - - - - - - 25 - TGCGATCT - 6 - - - - - - 26 - TTCCTGCT - 6 - - - - - - 27 - TAGTGACT - 6 - - - - - - 28 - TACAGGAT - 6 - - - - - - 29 - TCCTCAAT - 6 - - - - - - 30 - TGTGGTTG - 6 - - - - - - 31 - TAGTCTTG - 6 - - - - - - 32 - TTCCATTG - 6 - - - - - - 33 - TCGAAGTG - 6 - - - - - - 34 - TAACGCTG - 6 - - - - - - 35 - TTGGTATG - 6 - - - - - - 36 - TGAACTGG - 6 - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - diff --git a/t/data/st_api_lims_new/st/projects/429.xml b/t/data/st_api_lims_new/st/projects/429.xml deleted file mode 100644 index 265eb596..00000000 --- a/t/data/st_api_lims_new/st/projects/429.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - 429 - 3C and HiC of Plasmodium falciparum IT - true - active - - - External funding source - - - - Project cost code - S0701 - - - Sequencing budget cost centre - - - - Genotyping committee Tracking ID - - - - Collaborators - Prof. Chris Newbold - - - Funding comments - - - - Project funding model - Internal - - - diff --git a/t/data/st_api_lims_new/st/projects/810.xml b/t/data/st_api_lims_new/st/projects/810.xml deleted file mode 100644 index fd5b3290..00000000 --- a/t/data/st_api_lims_new/st/projects/810.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - 810 - Schistosoma mansoni methylome - true - active - - - External funding source - - - - Project cost code - S0702 - - - Sequencing budget cost centre - - - - Genotyping committee Tracking ID - - - - Collaborators - Karl Hoffmann - - - Funding comments - - - - Project funding model - Internal - - - diff --git a/t/data/st_api_lims_new/st/samples/1060341.xml b/t/data/st_api_lims_new/st/samples/1060341.xml deleted file mode 100644 index d92ac203..00000000 --- a/t/data/st_api_lims_new/st/samples/1060341.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1060341 - SMRU152 - 1703 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - - - - Common Name - Streptococcus pneumoniae - - - Strain - NT - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS019310 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 1703 - diff --git a/t/data/st_api_lims_new/st/samples/10881.xml b/t/data/st_api_lims_new/st/samples/10881.xml deleted file mode 100644 index aef5acbc..00000000 --- a/t/data/st_api_lims_new/st/samples/10881.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 10881 - H083280501 - 427 - - - Phenotype - - - - Sample purified - - - - TAXON ID - 224729 - - - Country of origin - - - - Treatment - - - - Time Point - - - - Date of sample extraction - - - - Sample Description - - - - ENA Sample Accession Number - ERS003167 - - - Common Name - Salmonella enterica subsp. enterica serovar Java - - - Gender - - - - Mother - - - - Ethnicity - - - - Compound - - - - Cell Type - - - - Age - - - - Genotype - - - - Volume (µl) - - - - Dose - - - - Organism Part - - - - Growth Condition - - - - Concentration - - - - Public Name - H083280501 - - - Subject - - - - RNAi - - - - Concentration determind by - - - - Is re-submitted? - - - - DNA source - - - - Sample extraction method - - - - Disease - - - - Sibling - - - - Strain - S java - - - Cohort - - - - Immunoprecipitate - - - - Disease State - - - - Sample storage conditions - - - - Sample type - - - - Date of sample collection - - - - Developmental Stage - - - - Purification method - - - - Sample Visibility - Hold - - - GC content - neutral - - - Father - - - - Plate - - - - Geographical region - - - - Replicate - - - - Organism - Salmonella enterica Java - - - Reference Genome - - - - - - - - - - 427 - diff --git a/t/data/st_api_lims_new/st/samples/1093797.xml b/t/data/st_api_lims_new/st/samples/1093797.xml deleted file mode 100644 index 93728f12..00000000 --- a/t/data/st_api_lims_new/st/samples/1093797.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093797 - RPR_ND - 1772 - false - - - Organism - human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - 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ERS024591 - - - TAXON ID - 624 - - - Strain - 109305 - - - Common Name - Shigella sonnei - - - Public Name - SS109305 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093819.xml b/t/data/st_api_lims_new/st/samples/1093819.xml deleted file mode 100644 index e67d173d..00000000 --- a/t/data/st_api_lims_new/st/samples/1093819.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093819 - SS109114 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - 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- - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093821.xml b/t/data/st_api_lims_new/st/samples/1093821.xml deleted file mode 100644 index e022c09b..00000000 --- a/t/data/st_api_lims_new/st/samples/1093821.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093821 - SS117077 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024594 - - - TAXON ID - 624 - - - Strain - 117077 - - - Common Name - Shigella sonnei - - - Public Name - SS117077 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093822.xml b/t/data/st_api_lims_new/st/samples/1093822.xml deleted file mode 100644 index f994d893..00000000 --- a/t/data/st_api_lims_new/st/samples/1093822.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093822 - SS127358 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - 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ERS024596 - - - TAXON ID - 624 - - - Strain - 129050 - - - Common Name - Shigella sonnei - - - Public Name - SS129050 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093824.xml b/t/data/st_api_lims_new/st/samples/1093824.xml deleted file mode 100644 index 8be8b68b..00000000 --- a/t/data/st_api_lims_new/st/samples/1093824.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093824 - SS127858 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024597 - - - TAXON ID - 624 - - - Strain - 127858 - - - Common Name - Shigella sonnei - - - Public Name - SS127858 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093825.xml b/t/data/st_api_lims_new/st/samples/1093825.xml deleted file mode 100644 index 77841f24..00000000 --- a/t/data/st_api_lims_new/st/samples/1093825.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093825 - SS128220 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024598 - - - TAXON ID - 624 - - - Strain - 128220 - - - Common Name - Shigella sonnei - - - Public Name - SS128220 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093826.xml b/t/data/st_api_lims_new/st/samples/1093826.xml deleted file mode 100644 index 4c787d8d..00000000 --- a/t/data/st_api_lims_new/st/samples/1093826.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093826 - SS128716 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024599 - - - TAXON ID - 624 - - - Strain - 128716 - - - Common Name - Shigella sonnei - - - Public Name - SS128716 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093827.xml b/t/data/st_api_lims_new/st/samples/1093827.xml deleted file mode 100644 index fe1ff621..00000000 --- a/t/data/st_api_lims_new/st/samples/1093827.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093827 - SS129764 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024600 - - - TAXON ID - 624 - - - Strain - 129764 - - - Common Name - Shigella sonnei - - - Public Name - SS129764 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093828.xml b/t/data/st_api_lims_new/st/samples/1093828.xml deleted file mode 100644 index f809c8eb..00000000 --- a/t/data/st_api_lims_new/st/samples/1093828.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093828 - SS130327 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024601 - - - TAXON ID - 624 - - - Strain - 130327 - - - Common Name - Shigella sonnei - - - Public Name - SS130327 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/1093829.xml b/t/data/st_api_lims_new/st/samples/1093829.xml deleted file mode 100644 index 6ad60bdf..00000000 --- a/t/data/st_api_lims_new/st/samples/1093829.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1093829 - SS131636 - 297 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Shigella sonnei - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS024602 - - - TAXON ID - 624 - - - Strain - 131636 - - - Common Name - Shigella sonnei - - - Public Name - SS131636 - - - Age - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/st_api_lims_new/st/samples/11036.xml b/t/data/st_api_lims_new/st/samples/11036.xml deleted file mode 100644 index a1808557..00000000 --- a/t/data/st_api_lims_new/st/samples/11036.xml +++ /dev/null @@ -1,207 +0,0 @@ - - - 11036 - Keith1 - 440 - false - - - Phenotype - - - - Sample purified - - - - TAXON ID - 90370 - - - Country of origin - - - - Treatment - - - - Time Point - - - - Date of sample extraction - - - - Sample Description - TraDIS library - - - ENA Sample Accession Number - ERS003242 - - - Common Name - Salmonella enterica subsp. enterica serovar Typhi - - - Gender - - - - Mother - - - - Ethnicity - - - - Compound - - - - Cell Type - - - - Age - - - - Genotype - - - - Volume (µl) - - - - Dose - - - - Organism Part - - - - Growth Condition - - - - Concentration - - - - Public Name - Ctrl1 - - - Subject - - - - RNAi - - - - Concentration determind by - - - - Is re-submitted? - - - - DNA source - - - - Sample extraction method - - - - Disease - - - - Sibling - - - - Strain - CVD908-htrA - - - Cohort - - - - Immunoprecipitate - - - - Disease State - - - - Sample storage conditions - - - - Sample type - - - - Date of sample collection - - - - Developmental Stage - - - - Purification method - - - - Sample Visibility - Hold - - - GC content - neutral - - - Father - - - - Plate - - - - Geographical region - - - - Replicate - - - - Organism - Salmonella typhi - - - Reference Genome - - - - - - - - - 440 - diff --git a/t/data/st_api_lims_new/st/samples/1118234.xml b/t/data/st_api_lims_new/st/samples/1118234.xml deleted file mode 100644 index 16830c7a..00000000 --- a/t/data/st_api_lims_new/st/samples/1118234.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118234 - SN27041 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27041 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069155 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118235.xml b/t/data/st_api_lims_new/st/samples/1118235.xml deleted file mode 100644 index 744a4c8c..00000000 --- a/t/data/st_api_lims_new/st/samples/1118235.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118235 - SN27071 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27071 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069156 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118236.xml b/t/data/st_api_lims_new/st/samples/1118236.xml deleted file mode 100644 index bb44ed67..00000000 --- a/t/data/st_api_lims_new/st/samples/1118236.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118236 - SN27072 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27072 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069157 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118237.xml b/t/data/st_api_lims_new/st/samples/1118237.xml deleted file mode 100644 index a50ac9f7..00000000 --- a/t/data/st_api_lims_new/st/samples/1118237.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118237 - SN27110 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27110 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069158 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118238.xml b/t/data/st_api_lims_new/st/samples/1118238.xml deleted file mode 100644 index e2d4113f..00000000 --- a/t/data/st_api_lims_new/st/samples/1118238.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118238 - SN27111 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27111 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069159 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118239.xml b/t/data/st_api_lims_new/st/samples/1118239.xml deleted file mode 100644 index 10548c31..00000000 --- a/t/data/st_api_lims_new/st/samples/1118239.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118239 - SN27402 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27402 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069160 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118240.xml b/t/data/st_api_lims_new/st/samples/1118240.xml deleted file mode 100644 index 73f0dffd..00000000 --- a/t/data/st_api_lims_new/st/samples/1118240.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118240 - SN27457 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27457 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069161 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118241.xml b/t/data/st_api_lims_new/st/samples/1118241.xml deleted file mode 100644 index 0f4a8b90..00000000 --- a/t/data/st_api_lims_new/st/samples/1118241.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118241 - SN27467 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27467 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069162 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118242.xml b/t/data/st_api_lims_new/st/samples/1118242.xml deleted file mode 100644 index 379e91df..00000000 --- a/t/data/st_api_lims_new/st/samples/1118242.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118242 - SN27518 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27518 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069163 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118243.xml b/t/data/st_api_lims_new/st/samples/1118243.xml deleted file mode 100644 index f51de24e..00000000 --- a/t/data/st_api_lims_new/st/samples/1118243.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118243 - SN27556 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27556 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069164 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118244.xml b/t/data/st_api_lims_new/st/samples/1118244.xml deleted file mode 100644 index 9cdda408..00000000 --- a/t/data/st_api_lims_new/st/samples/1118244.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118244 - SN27673 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27673 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069165 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118245.xml b/t/data/st_api_lims_new/st/samples/1118245.xml deleted file mode 100644 index 0a8686da..00000000 --- a/t/data/st_api_lims_new/st/samples/1118245.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118245 - SN27684 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27684 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069166 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118246.xml b/t/data/st_api_lims_new/st/samples/1118246.xml deleted file mode 100644 index c9860119..00000000 --- a/t/data/st_api_lims_new/st/samples/1118246.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118246 - SN27815 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27815 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069167 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118247.xml b/t/data/st_api_lims_new/st/samples/1118247.xml deleted file mode 100644 index 27479b07..00000000 --- a/t/data/st_api_lims_new/st/samples/1118247.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118247 - SN27818 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27818 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069168 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118248.xml b/t/data/st_api_lims_new/st/samples/1118248.xml deleted file mode 100644 index 4096dcab..00000000 --- a/t/data/st_api_lims_new/st/samples/1118248.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118248 - SN27857 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27857 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069169 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118249.xml b/t/data/st_api_lims_new/st/samples/1118249.xml deleted file mode 100644 index bd409151..00000000 --- a/t/data/st_api_lims_new/st/samples/1118249.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118249 - SN27903 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN27903 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069170 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118250.xml b/t/data/st_api_lims_new/st/samples/1118250.xml deleted file mode 100644 index 19d240db..00000000 --- a/t/data/st_api_lims_new/st/samples/1118250.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118250 - SN28019 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28019 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069171 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118251.xml b/t/data/st_api_lims_new/st/samples/1118251.xml deleted file mode 100644 index 1b8a25c1..00000000 --- a/t/data/st_api_lims_new/st/samples/1118251.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118251 - SN28054 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28054 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069172 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118252.xml b/t/data/st_api_lims_new/st/samples/1118252.xml deleted file mode 100644 index 4f75495a..00000000 --- a/t/data/st_api_lims_new/st/samples/1118252.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118252 - SN28129 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28129 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069173 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118253.xml b/t/data/st_api_lims_new/st/samples/1118253.xml deleted file mode 100644 index 48b1f939..00000000 --- a/t/data/st_api_lims_new/st/samples/1118253.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118253 - SN28162 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28162 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069174 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118254.xml b/t/data/st_api_lims_new/st/samples/1118254.xml deleted file mode 100644 index b9f2351b..00000000 --- a/t/data/st_api_lims_new/st/samples/1118254.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118254 - SN28177 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28177 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069175 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118255.xml b/t/data/st_api_lims_new/st/samples/1118255.xml deleted file mode 100644 index 3baa8e28..00000000 --- a/t/data/st_api_lims_new/st/samples/1118255.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118255 - SN28222 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28222 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069176 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118256.xml b/t/data/st_api_lims_new/st/samples/1118256.xml deleted file mode 100644 index a1ac3c2b..00000000 --- a/t/data/st_api_lims_new/st/samples/1118256.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118256 - SN28230 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28230 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069177 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118257.xml b/t/data/st_api_lims_new/st/samples/1118257.xml deleted file mode 100644 index ac333064..00000000 --- a/t/data/st_api_lims_new/st/samples/1118257.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118257 - SN28293 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28293 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069178 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118258.xml b/t/data/st_api_lims_new/st/samples/1118258.xml deleted file mode 100644 index b48aebed..00000000 --- a/t/data/st_api_lims_new/st/samples/1118258.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118258 - SN28419 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28419 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069179 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118259.xml b/t/data/st_api_lims_new/st/samples/1118259.xml deleted file mode 100644 index ca8b472b..00000000 --- a/t/data/st_api_lims_new/st/samples/1118259.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118259 - SN28421 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28421 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069180 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118260.xml b/t/data/st_api_lims_new/st/samples/1118260.xml deleted file mode 100644 index 28e7b1ce..00000000 --- a/t/data/st_api_lims_new/st/samples/1118260.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118260 - SN28481 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28481 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069181 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118261.xml b/t/data/st_api_lims_new/st/samples/1118261.xml deleted file mode 100644 index fe186773..00000000 --- a/t/data/st_api_lims_new/st/samples/1118261.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118261 - SN28493 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28493 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069182 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118262.xml b/t/data/st_api_lims_new/st/samples/1118262.xml deleted file mode 100644 index c5ff21ba..00000000 --- a/t/data/st_api_lims_new/st/samples/1118262.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118262 - SN28582 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28582 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069183 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118263.xml b/t/data/st_api_lims_new/st/samples/1118263.xml deleted file mode 100644 index 0c65a90f..00000000 --- a/t/data/st_api_lims_new/st/samples/1118263.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118263 - SN28685 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28685 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069184 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118264.xml b/t/data/st_api_lims_new/st/samples/1118264.xml deleted file mode 100644 index 1659efda..00000000 --- a/t/data/st_api_lims_new/st/samples/1118264.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118264 - SN28699 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28699 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069185 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118265.xml b/t/data/st_api_lims_new/st/samples/1118265.xml deleted file mode 100644 index 511c5563..00000000 --- a/t/data/st_api_lims_new/st/samples/1118265.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118265 - SN28722 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28722 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069186 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118266.xml b/t/data/st_api_lims_new/st/samples/1118266.xml deleted file mode 100644 index 08815496..00000000 --- a/t/data/st_api_lims_new/st/samples/1118266.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118266 - SN28777 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28777 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069187 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118267.xml b/t/data/st_api_lims_new/st/samples/1118267.xml deleted file mode 100644 index 13a1a069..00000000 --- a/t/data/st_api_lims_new/st/samples/1118267.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118267 - SN28796 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28796 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069188 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118268.xml b/t/data/st_api_lims_new/st/samples/1118268.xml deleted file mode 100644 index f9165f2d..00000000 --- a/t/data/st_api_lims_new/st/samples/1118268.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118268 - SN28797 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28797 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069189 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118269.xml b/t/data/st_api_lims_new/st/samples/1118269.xml deleted file mode 100644 index 7785c3a8..00000000 --- a/t/data/st_api_lims_new/st/samples/1118269.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118269 - SN28854 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28854 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069190 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118270.xml b/t/data/st_api_lims_new/st/samples/1118270.xml deleted file mode 100644 index f71cc853..00000000 --- a/t/data/st_api_lims_new/st/samples/1118270.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118270 - SN28890 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28890 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069191 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118271.xml b/t/data/st_api_lims_new/st/samples/1118271.xml deleted file mode 100644 index 901a56ae..00000000 --- a/t/data/st_api_lims_new/st/samples/1118271.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118271 - SN28905 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28905 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069192 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118272.xml b/t/data/st_api_lims_new/st/samples/1118272.xml deleted file mode 100644 index 69495d4e..00000000 --- a/t/data/st_api_lims_new/st/samples/1118272.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118272 - SN28918 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28918 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069193 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118273.xml b/t/data/st_api_lims_new/st/samples/1118273.xml deleted file mode 100644 index 72ea50f4..00000000 --- a/t/data/st_api_lims_new/st/samples/1118273.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118273 - SN28923 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28923 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069194 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118274.xml b/t/data/st_api_lims_new/st/samples/1118274.xml deleted file mode 100644 index 47276387..00000000 --- a/t/data/st_api_lims_new/st/samples/1118274.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118274 - SN28974 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28974 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069195 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118275.xml b/t/data/st_api_lims_new/st/samples/1118275.xml deleted file mode 100644 index 3ccae32d..00000000 --- a/t/data/st_api_lims_new/st/samples/1118275.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118275 - SN28994 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN28994 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069196 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118276.xml b/t/data/st_api_lims_new/st/samples/1118276.xml deleted file mode 100644 index 4f697b92..00000000 --- a/t/data/st_api_lims_new/st/samples/1118276.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118276 - SN29738 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN29738 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069197 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118277.xml b/t/data/st_api_lims_new/st/samples/1118277.xml deleted file mode 100644 index 06d79fc5..00000000 --- a/t/data/st_api_lims_new/st/samples/1118277.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118277 - SN29754 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN29754 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069198 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118278.xml b/t/data/st_api_lims_new/st/samples/1118278.xml deleted file mode 100644 index 8bcd8f2a..00000000 --- a/t/data/st_api_lims_new/st/samples/1118278.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118278 - SN29770 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN29770 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069199 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118279.xml b/t/data/st_api_lims_new/st/samples/1118279.xml deleted file mode 100644 index 44db1631..00000000 --- a/t/data/st_api_lims_new/st/samples/1118279.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118279 - SN29791 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN29791 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069200 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118280.xml b/t/data/st_api_lims_new/st/samples/1118280.xml deleted file mode 100644 index f9183a7e..00000000 --- a/t/data/st_api_lims_new/st/samples/1118280.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118280 - SN29798 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN29798 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069201 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1118281.xml b/t/data/st_api_lims_new/st/samples/1118281.xml deleted file mode 100644 index 292fdfba..00000000 --- a/t/data/st_api_lims_new/st/samples/1118281.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1118281 - SN29801 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SN29801 - - - Common Name - Streptococcus pneumoniae - - - Strain - - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069202 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1121926.xml b/t/data/st_api_lims_new/st/samples/1121926.xml deleted file mode 100644 index 32c5169c..00000000 --- a/t/data/st_api_lims_new/st/samples/1121926.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1121926 - BS_3hrsomuleSm_202790 - 1811 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Mixed - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - Neutral - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Schistosoma mansoni - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS028649 - - - TAXON ID - 6183 - - - Strain - Puerto Rican - - - Common Name - Schistosoma mansoni - - - Public Name - - - - Age - - - - Reference Genome - Schistosoma_mansoni (20100601) - - - - - - - - - - 1811 - diff --git a/t/data/st_api_lims_new/st/samples/1132331.xml b/t/data/st_api_lims_new/st/samples/1132331.xml deleted file mode 100644 index 932eb61b..00000000 --- a/t/data/st_api_lims_new/st/samples/1132331.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132331 - HiC_H_ON_DCJ - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033158 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132333.xml b/t/data/st_api_lims_new/st/samples/1132333.xml deleted file mode 100644 index c9cd4309..00000000 --- a/t/data/st_api_lims_new/st/samples/1132333.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132333 - HiC_H_Dd2 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033160 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132335.xml b/t/data/st_api_lims_new/st/samples/1132335.xml deleted file mode 100644 index 66cf85fb..00000000 --- a/t/data/st_api_lims_new/st/samples/1132335.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132335 - HiC_H_PQP1 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033162 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132341.xml b/t/data/st_api_lims_new/st/samples/1132341.xml deleted file mode 100644 index e165913b..00000000 --- a/t/data/st_api_lims_new/st/samples/1132341.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132341 - HiC_H_OFF_DCJ - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033168 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132343.xml b/t/data/st_api_lims_new/st/samples/1132343.xml deleted file mode 100644 index 39c37217..00000000 --- a/t/data/st_api_lims_new/st/samples/1132343.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132343 - HIC_M_B15C2 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033170 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132345.xml b/t/data/st_api_lims_new/st/samples/1132345.xml deleted file mode 100644 index afa1e422..00000000 --- a/t/data/st_api_lims_new/st/samples/1132345.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132345 - HiC_M_Rev1 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033172 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132347.xml b/t/data/st_api_lims_new/st/samples/1132347.xml deleted file mode 100644 index 5f85ae6a..00000000 --- a/t/data/st_api_lims_new/st/samples/1132347.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132347 - HiC_M_3D7 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033174 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132349.xml b/t/data/st_api_lims_new/st/samples/1132349.xml deleted file mode 100644 index 0c9dabc9..00000000 --- a/t/data/st_api_lims_new/st/samples/1132349.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132349 - HiC_M_ER3D7 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033176 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1132351.xml b/t/data/st_api_lims_new/st/samples/1132351.xml deleted file mode 100644 index 1bfdbf77..00000000 --- a/t/data/st_api_lims_new/st/samples/1132351.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 1132351 - HiC_H_LT3D7 - 429 - - - Disease - - - - Subject - - - - Treatment - - - - Time Point - - - - Organism Part - - - - RNAi - - - - Growth Condition - - - - Immunoprecipitate - - - - DNA source - Genomic - - - Geographical region - - - - Compound - - - - Disease State - - - - Cell Type - - - - Developmental Stage - - - - Gender - Not Applicable - - - Volume (µl) - - - - Country of origin - - - - Phenotype - - - - Genotype - - - - Sample storage conditions - - - - Sample type - - - - Concentration determind by - - - - Concentration - - - - Purification method - - - - Sample purified - - - - Sample extraction method - - - - Date of sample extraction - - - - Date of sample collection - - - - Is re-submitted? - - - - Sibling - - - - Cohort - - - - Dose - - - - GC content - High AT - - - Replicate - - - - Father - - - - Mother - - - - Plate - - - - Ethnicity - - - - Organism - Plasmodium falciparum - - - Sample Visibility - Hold - - - Sample Description - - - - ENA Sample Accession Number - ERS033178 - - - TAXON ID - 5833 - - - Strain - - - - Common Name - Plasmodium falciparum - - - Public Name - - - - Age - - - - Reference Genome - - - - - - - - - - - 429 - diff --git a/t/data/st_api_lims_new/st/samples/1135847.xml b/t/data/st_api_lims_new/st/samples/1135847.xml deleted file mode 100644 index 84765baa..00000000 --- a/t/data/st_api_lims_new/st/samples/1135847.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135847 - SH0090 - 1826 - false - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - IB1644 - - - Gender - Not Applicable - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - Shigella flexneri - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 623 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - ERS033304 - - - Strain - IB1644 - - - GC content - Neutral - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Age - - - - Sample Description - - - - Common Name - Shigella flexneri - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135848.xml b/t/data/st_api_lims_new/st/samples/1135848.xml deleted file mode 100644 index 9ef5391a..00000000 --- a/t/data/st_api_lims_new/st/samples/1135848.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135848 - SH0091 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1645 - - - Common Name - Shigella flexneri - - - Strain - IB1645 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033305 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135849.xml b/t/data/st_api_lims_new/st/samples/1135849.xml deleted file mode 100644 index 3aa510a7..00000000 --- a/t/data/st_api_lims_new/st/samples/1135849.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135849 - SH0092 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1646 - - - Common Name - Shigella flexneri - - - Strain - IB1646 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033306 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135850.xml b/t/data/st_api_lims_new/st/samples/1135850.xml deleted file mode 100644 index 9f91cddc..00000000 --- a/t/data/st_api_lims_new/st/samples/1135850.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135850 - SH0093 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1647 - - - Common Name - Shigella flexneri - - - Strain - IB1647 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033307 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135851.xml b/t/data/st_api_lims_new/st/samples/1135851.xml deleted file mode 100644 index 087eb20c..00000000 --- a/t/data/st_api_lims_new/st/samples/1135851.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135851 - SH0094 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1648 - - - Common Name - Shigella flexneri - - - Strain - IB1648 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033308 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135852.xml b/t/data/st_api_lims_new/st/samples/1135852.xml deleted file mode 100644 index 85e79ca3..00000000 --- a/t/data/st_api_lims_new/st/samples/1135852.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135852 - SH0095 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1649 - - - Common Name - Shigella flexneri - - - Strain - IB1649 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033309 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135853.xml b/t/data/st_api_lims_new/st/samples/1135853.xml deleted file mode 100644 index a2826e18..00000000 --- a/t/data/st_api_lims_new/st/samples/1135853.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135853 - SH0096 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1650 - - - Common Name - Shigella flexneri - - - Strain - IB1650 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033310 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135854.xml b/t/data/st_api_lims_new/st/samples/1135854.xml deleted file mode 100644 index aadf873f..00000000 --- a/t/data/st_api_lims_new/st/samples/1135854.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135854 - SH0097 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1651 - - - Common Name - Shigella flexneri - - - Strain - IB1651 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033311 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135855.xml b/t/data/st_api_lims_new/st/samples/1135855.xml deleted file mode 100644 index 30b5898f..00000000 --- a/t/data/st_api_lims_new/st/samples/1135855.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135855 - SH0098 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1652 - - - Common Name - Shigella flexneri - - - Strain - IB1652 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033312 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135856.xml b/t/data/st_api_lims_new/st/samples/1135856.xml deleted file mode 100644 index cc019185..00000000 --- a/t/data/st_api_lims_new/st/samples/1135856.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135856 - SH0099 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1653 - - - Common Name - Shigella flexneri - - - Strain - IB1653 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033313 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135857.xml b/t/data/st_api_lims_new/st/samples/1135857.xml deleted file mode 100644 index 151c136f..00000000 --- a/t/data/st_api_lims_new/st/samples/1135857.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135857 - SH0100 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1654 - - - Common Name - Shigella flexneri - - - Strain - IB1654 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033314 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135858.xml b/t/data/st_api_lims_new/st/samples/1135858.xml deleted file mode 100644 index 922ef444..00000000 --- a/t/data/st_api_lims_new/st/samples/1135858.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135858 - SH0101 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1655 - - - Common Name - Shigella flexneri - - - Strain - IB1655 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033315 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135859.xml b/t/data/st_api_lims_new/st/samples/1135859.xml deleted file mode 100644 index 293abbca..00000000 --- a/t/data/st_api_lims_new/st/samples/1135859.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135859 - SH0102 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1656 - - - Common Name - Shigella flexneri - - - Strain - IB1656 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033316 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135860.xml b/t/data/st_api_lims_new/st/samples/1135860.xml deleted file mode 100644 index 78336b70..00000000 --- a/t/data/st_api_lims_new/st/samples/1135860.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135860 - SH0103 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1657 - - - Common Name - Shigella flexneri - - - Strain - IB1657 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033317 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135861.xml b/t/data/st_api_lims_new/st/samples/1135861.xml deleted file mode 100644 index 59eda8ec..00000000 --- a/t/data/st_api_lims_new/st/samples/1135861.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135861 - SH0104 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1658 - - - Common Name - Shigella flexneri - - - Strain - IB1658 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033318 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135862.xml b/t/data/st_api_lims_new/st/samples/1135862.xml deleted file mode 100644 index a73427a2..00000000 --- a/t/data/st_api_lims_new/st/samples/1135862.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135862 - SH0105 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1659 - - - Common Name - Shigella flexneri - - - Strain - IB1659 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033319 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135863.xml b/t/data/st_api_lims_new/st/samples/1135863.xml deleted file mode 100644 index 2e4c2620..00000000 --- a/t/data/st_api_lims_new/st/samples/1135863.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135863 - SH0106 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1660 - - - Common Name - Shigella flexneri - - - Strain - IB1660 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033320 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135864.xml b/t/data/st_api_lims_new/st/samples/1135864.xml deleted file mode 100644 index bf5c5ac1..00000000 --- a/t/data/st_api_lims_new/st/samples/1135864.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135864 - SH0107 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1661 - - - Common Name - Shigella flexneri - - - Strain - IB1661 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033321 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135865.xml b/t/data/st_api_lims_new/st/samples/1135865.xml deleted file mode 100644 index 2f4a1e53..00000000 --- a/t/data/st_api_lims_new/st/samples/1135865.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135865 - SH0108 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1662 - - - Common Name - Shigella flexneri - - - Strain - IB1662 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033322 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135866.xml b/t/data/st_api_lims_new/st/samples/1135866.xml deleted file mode 100644 index 0dec9f44..00000000 --- a/t/data/st_api_lims_new/st/samples/1135866.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135866 - SH0109 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1663 - - - Common Name - Shigella flexneri - - - Strain - IB1663 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033323 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135867.xml b/t/data/st_api_lims_new/st/samples/1135867.xml deleted file mode 100644 index e216eebd..00000000 --- a/t/data/st_api_lims_new/st/samples/1135867.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135867 - SH0110 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1664 - - - Common Name - Shigella flexneri - - - Strain - IB1664 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033324 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135868.xml b/t/data/st_api_lims_new/st/samples/1135868.xml deleted file mode 100644 index 14cf1c6d..00000000 --- a/t/data/st_api_lims_new/st/samples/1135868.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135868 - SH0111 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1665 - - - Common Name - Shigella flexneri - - - Strain - IB1665 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033325 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135869.xml b/t/data/st_api_lims_new/st/samples/1135869.xml deleted file mode 100644 index 4f1923a9..00000000 --- a/t/data/st_api_lims_new/st/samples/1135869.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135869 - SH0112 - 1826 - false - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - IB1666 - - - Gender - Not Applicable - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - Shigella flexneri - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 623 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - ERS033326 - - - Strain - IB1666 - - - GC content - Neutral - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Age - - - - Sample Description - - - - Common Name - Shigella flexneri - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135870.xml b/t/data/st_api_lims_new/st/samples/1135870.xml deleted file mode 100644 index 6373141b..00000000 --- a/t/data/st_api_lims_new/st/samples/1135870.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135870 - SH0113 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1667 - - - Common Name - Shigella flexneri - - - Strain - IB1667 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033327 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135871.xml b/t/data/st_api_lims_new/st/samples/1135871.xml deleted file mode 100644 index 2d529480..00000000 --- a/t/data/st_api_lims_new/st/samples/1135871.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135871 - SH0114 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1668 - - - Common Name - Shigella flexneri - - - Strain - IB1668 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033328 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135872.xml b/t/data/st_api_lims_new/st/samples/1135872.xml deleted file mode 100644 index c876a60a..00000000 --- a/t/data/st_api_lims_new/st/samples/1135872.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135872 - SH0115 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1669 - - - Common Name - Shigella flexneri - - - Strain - IB1669 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033329 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135873.xml b/t/data/st_api_lims_new/st/samples/1135873.xml deleted file mode 100644 index 17ae4d08..00000000 --- a/t/data/st_api_lims_new/st/samples/1135873.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135873 - SH0116 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1670 - - - Common Name - Shigella flexneri - - - Strain - IB1670 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033330 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135874.xml b/t/data/st_api_lims_new/st/samples/1135874.xml deleted file mode 100644 index 021fcd2f..00000000 --- a/t/data/st_api_lims_new/st/samples/1135874.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135874 - SH0117 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB2490 - - - Common Name - Shigella flexneri - - - Strain - IB2490 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033331 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135875.xml b/t/data/st_api_lims_new/st/samples/1135875.xml deleted file mode 100644 index 765e08b9..00000000 --- a/t/data/st_api_lims_new/st/samples/1135875.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135875 - SH0118 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB2491 - - - Common Name - Shigella flexneri - - - Strain - IB2491 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033332 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135876.xml b/t/data/st_api_lims_new/st/samples/1135876.xml deleted file mode 100644 index d41353e1..00000000 --- a/t/data/st_api_lims_new/st/samples/1135876.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135876 - SH0119 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1685 - - - Common Name - Shigella flexneri - - - Strain - IB1685 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033333 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135877.xml b/t/data/st_api_lims_new/st/samples/1135877.xml deleted file mode 100644 index db78a177..00000000 --- a/t/data/st_api_lims_new/st/samples/1135877.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135877 - SH0120 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1721 - - - Common Name - Shigella flexneri - - - Strain - IB1721 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033334 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135878.xml b/t/data/st_api_lims_new/st/samples/1135878.xml deleted file mode 100644 index 85d3a5fa..00000000 --- a/t/data/st_api_lims_new/st/samples/1135878.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135878 - SH0121 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1788 - - - Common Name - Shigella flexneri - - - Strain - IB1788 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033335 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135879.xml b/t/data/st_api_lims_new/st/samples/1135879.xml deleted file mode 100644 index 0d778cde..00000000 --- a/t/data/st_api_lims_new/st/samples/1135879.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135879 - SH0122 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1789 - - - Common Name - Shigella flexneri - - - Strain - IB1789 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033336 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135880.xml b/t/data/st_api_lims_new/st/samples/1135880.xml deleted file mode 100644 index 2de2d2d1..00000000 --- a/t/data/st_api_lims_new/st/samples/1135880.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135880 - SH0123 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1835 - - - Common Name - Shigella flexneri - - - Strain - IB1835 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033337 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135881.xml b/t/data/st_api_lims_new/st/samples/1135881.xml deleted file mode 100644 index 43fb6dad..00000000 --- a/t/data/st_api_lims_new/st/samples/1135881.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135881 - SH0124 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1885 - - - Common Name - Shigella flexneri - - - Strain - IB1885 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033338 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135882.xml b/t/data/st_api_lims_new/st/samples/1135882.xml deleted file mode 100644 index 1630a575..00000000 --- a/t/data/st_api_lims_new/st/samples/1135882.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135882 - SH0125 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB4230 - - - Common Name - Shigella flexneri - - - Strain - IB4230 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033339 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - 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- - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135884.xml b/t/data/st_api_lims_new/st/samples/1135884.xml deleted file mode 100644 index 3361d230..00000000 --- a/t/data/st_api_lims_new/st/samples/1135884.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135884 - SH0127 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3327 - - - Common Name - Shigella flexneri - - - Strain - IB3327 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033341 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135885.xml b/t/data/st_api_lims_new/st/samples/1135885.xml deleted file mode 100644 index b165713b..00000000 --- a/t/data/st_api_lims_new/st/samples/1135885.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135885 - SH0128 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3328 - - - Common Name - Shigella flexneri - - - Strain - IB3328 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033342 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135886.xml b/t/data/st_api_lims_new/st/samples/1135886.xml deleted file mode 100644 index aa386b5a..00000000 --- a/t/data/st_api_lims_new/st/samples/1135886.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135886 - SH0129 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3350 - - - Common Name - Shigella flexneri - - - Strain - IB3350 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033343 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135887.xml b/t/data/st_api_lims_new/st/samples/1135887.xml deleted file mode 100644 index 70b5b880..00000000 --- a/t/data/st_api_lims_new/st/samples/1135887.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135887 - SH0130 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3356 - - - Common Name - Shigella flexneri - - - Strain - IB3356 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033344 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135888.xml b/t/data/st_api_lims_new/st/samples/1135888.xml deleted file mode 100644 index 0d62ee63..00000000 --- a/t/data/st_api_lims_new/st/samples/1135888.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135888 - SH0131 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3371 - - - Common Name - Shigella flexneri - - - Strain - IB3371 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033345 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135889.xml b/t/data/st_api_lims_new/st/samples/1135889.xml deleted file mode 100644 index 9130f000..00000000 --- a/t/data/st_api_lims_new/st/samples/1135889.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135889 - SH0132 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3389 - - - Common Name - Shigella flexneri - - - Strain - IB3389 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033346 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135890.xml b/t/data/st_api_lims_new/st/samples/1135890.xml deleted file mode 100644 index 19b86f21..00000000 --- a/t/data/st_api_lims_new/st/samples/1135890.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135890 - SH0133 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3391 - - - Common Name - Shigella flexneri - - - Strain - IB3391 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033347 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135891.xml b/t/data/st_api_lims_new/st/samples/1135891.xml deleted file mode 100644 index 9e7201ff..00000000 --- a/t/data/st_api_lims_new/st/samples/1135891.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135891 - SH0134 - 1826 - false - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - IB3396 - - - Gender - Not Applicable - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - Shigella flexneri - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 623 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - ERS033348 - - - Strain - IB3396 - - - GC content - Neutral - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Age - - - - Sample Description - - - - Common Name - Shigella flexneri - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135892.xml b/t/data/st_api_lims_new/st/samples/1135892.xml deleted file mode 100644 index 4749fc9a..00000000 --- a/t/data/st_api_lims_new/st/samples/1135892.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135892 - SH0135 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3404 - - - Common Name - Shigella flexneri - - - Strain - IB3404 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033349 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135893.xml b/t/data/st_api_lims_new/st/samples/1135893.xml deleted file mode 100644 index 2fb35917..00000000 --- a/t/data/st_api_lims_new/st/samples/1135893.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135893 - SH0136 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3432 - - - Common Name - Shigella flexneri - - - Strain - IB3432 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033350 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135894.xml b/t/data/st_api_lims_new/st/samples/1135894.xml deleted file mode 100644 index ce057fdd..00000000 --- a/t/data/st_api_lims_new/st/samples/1135894.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135894 - SH0137 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0700 - - - Common Name - Shigella flexneri - - - Strain - IB0700 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033351 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135895.xml b/t/data/st_api_lims_new/st/samples/1135895.xml deleted file mode 100644 index 0f473de1..00000000 --- a/t/data/st_api_lims_new/st/samples/1135895.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135895 - SH0138 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0708 - - - Common Name - Shigella flexneri - - - Strain - IB0708 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033352 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135896.xml b/t/data/st_api_lims_new/st/samples/1135896.xml deleted file mode 100644 index 28158875..00000000 --- a/t/data/st_api_lims_new/st/samples/1135896.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135896 - SH0139 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0709 - - - Common Name - Shigella flexneri - - - Strain - IB0709 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033353 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135897.xml b/t/data/st_api_lims_new/st/samples/1135897.xml deleted file mode 100644 index be265272..00000000 --- a/t/data/st_api_lims_new/st/samples/1135897.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135897 - SH0140 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0711 - - - Common Name - Shigella flexneri - - - Strain - IB0711 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033354 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135898.xml b/t/data/st_api_lims_new/st/samples/1135898.xml deleted file mode 100644 index 61af7f5c..00000000 --- a/t/data/st_api_lims_new/st/samples/1135898.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135898 - SH0141 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0712 - - - Common Name - Shigella flexneri - - - Strain - IB0712 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033355 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135899.xml b/t/data/st_api_lims_new/st/samples/1135899.xml deleted file mode 100644 index e4676c98..00000000 --- a/t/data/st_api_lims_new/st/samples/1135899.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135899 - SH0142 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0714 - - - Common Name - Shigella flexneri - - - Strain - IB0714 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033356 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135900.xml b/t/data/st_api_lims_new/st/samples/1135900.xml deleted file mode 100644 index 5b70974e..00000000 --- a/t/data/st_api_lims_new/st/samples/1135900.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135900 - SH0143 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0719 - - - Common Name - Shigella flexneri - - - Strain - IB0719 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033357 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135901.xml b/t/data/st_api_lims_new/st/samples/1135901.xml deleted file mode 100644 index 2f9a39e0..00000000 --- a/t/data/st_api_lims_new/st/samples/1135901.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135901 - SH0144 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0737 - - - Common Name - Shigella flexneri - - - Strain - IB0737 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033358 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135902.xml b/t/data/st_api_lims_new/st/samples/1135902.xml deleted file mode 100644 index 7846017f..00000000 --- a/t/data/st_api_lims_new/st/samples/1135902.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135902 - SH0145 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0740 - - - Common Name - Shigella flexneri - - - Strain - IB0740 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033359 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135903.xml b/t/data/st_api_lims_new/st/samples/1135903.xml deleted file mode 100644 index 49026eb8..00000000 --- a/t/data/st_api_lims_new/st/samples/1135903.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135903 - SH0146 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1709 - - - Common Name - Shigella flexneri - - - Strain - IB1709 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033360 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135904.xml b/t/data/st_api_lims_new/st/samples/1135904.xml deleted file mode 100644 index 90a9a1ae..00000000 --- a/t/data/st_api_lims_new/st/samples/1135904.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135904 - SH0147 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1808 - - - Common Name - Shigella flexneri - - - Strain - IB1808 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033361 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135905.xml b/t/data/st_api_lims_new/st/samples/1135905.xml deleted file mode 100644 index ce7eb305..00000000 --- a/t/data/st_api_lims_new/st/samples/1135905.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135905 - SH0148 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1848 - - - Common Name - Shigella flexneri - - - Strain - IB1848 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033362 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135906.xml b/t/data/st_api_lims_new/st/samples/1135906.xml deleted file mode 100644 index fab50318..00000000 --- a/t/data/st_api_lims_new/st/samples/1135906.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135906 - SH0149 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1896 - - - Common Name - Shigella flexneri - - - Strain - IB1896 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033363 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135907.xml b/t/data/st_api_lims_new/st/samples/1135907.xml deleted file mode 100644 index 5ccc7283..00000000 --- a/t/data/st_api_lims_new/st/samples/1135907.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135907 - SH0150 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB2494 - - - Common Name - Shigella flexneri - - - Strain - IB2494 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033364 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135908.xml b/t/data/st_api_lims_new/st/samples/1135908.xml deleted file mode 100644 index 334a78bb..00000000 --- a/t/data/st_api_lims_new/st/samples/1135908.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135908 - SH0151 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB2495 - - - Common Name - Shigella flexneri - - - Strain - IB2495 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033365 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135909.xml b/t/data/st_api_lims_new/st/samples/1135909.xml deleted file mode 100644 index 16567a94..00000000 --- a/t/data/st_api_lims_new/st/samples/1135909.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135909 - SH0152 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB2496 - - - Common Name - Shigella flexneri - - - Strain - IB2496 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033366 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135910.xml b/t/data/st_api_lims_new/st/samples/1135910.xml deleted file mode 100644 index bf7f13c0..00000000 --- a/t/data/st_api_lims_new/st/samples/1135910.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135910 - SH0153 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0011 - - - Common Name - Shigella flexneri - - - Strain - IB0011 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033367 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135911.xml b/t/data/st_api_lims_new/st/samples/1135911.xml deleted file mode 100644 index 910203da..00000000 --- a/t/data/st_api_lims_new/st/samples/1135911.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135911 - SH0154 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0012 - - - Common Name - Shigella flexneri - - - Strain - IB0012 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033368 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135912.xml b/t/data/st_api_lims_new/st/samples/1135912.xml deleted file mode 100644 index f67a27c7..00000000 --- a/t/data/st_api_lims_new/st/samples/1135912.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135912 - SH0155 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0017 - - - Common Name - Shigella flexneri - - - Strain - IB0017 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033369 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135913.xml b/t/data/st_api_lims_new/st/samples/1135913.xml deleted file mode 100644 index fed80856..00000000 --- a/t/data/st_api_lims_new/st/samples/1135913.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135913 - SH0156 - 1826 - false - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - IB0022 - - - Gender - Not Applicable - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - Shigella flexneri - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 623 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - ERS033370 - - - Strain - IB0022 - - - GC content - Neutral - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - - - - Age - - - - Sample Description - - - - Common Name - Shigella flexneri - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - - - - DNA source - Genomic - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135914.xml b/t/data/st_api_lims_new/st/samples/1135914.xml deleted file mode 100644 index b6dae5ee..00000000 --- a/t/data/st_api_lims_new/st/samples/1135914.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135914 - SH0157 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0034 - - - Common Name - Shigella flexneri - - - Strain - IB0034 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033371 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135915.xml b/t/data/st_api_lims_new/st/samples/1135915.xml deleted file mode 100644 index b75dc959..00000000 --- a/t/data/st_api_lims_new/st/samples/1135915.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135915 - SH0158 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0036 - - - Common Name - Shigella flexneri - - - Strain - IB0036 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033372 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135916.xml b/t/data/st_api_lims_new/st/samples/1135916.xml deleted file mode 100644 index 0dd031c3..00000000 --- a/t/data/st_api_lims_new/st/samples/1135916.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135916 - SH0159 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0037 - - - Common Name - Shigella flexneri - - - Strain - IB0037 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033373 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135917.xml b/t/data/st_api_lims_new/st/samples/1135917.xml deleted file mode 100644 index 8c992965..00000000 --- a/t/data/st_api_lims_new/st/samples/1135917.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135917 - SH0160 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0039 - - - Common Name - Shigella flexneri - - - Strain - IB0039 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033374 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135918.xml b/t/data/st_api_lims_new/st/samples/1135918.xml deleted file mode 100644 index d2428a16..00000000 --- a/t/data/st_api_lims_new/st/samples/1135918.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135918 - SH0161 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0043 - - - Common Name - Shigella flexneri - - - Strain - IB0043 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033375 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135919.xml b/t/data/st_api_lims_new/st/samples/1135919.xml deleted file mode 100644 index 203d41a9..00000000 --- a/t/data/st_api_lims_new/st/samples/1135919.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135919 - SH0162 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0045 - - - Common Name - Shigella flexneri - - - Strain - IB0045 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033376 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135920.xml b/t/data/st_api_lims_new/st/samples/1135920.xml deleted file mode 100644 index 4ea3224c..00000000 --- a/t/data/st_api_lims_new/st/samples/1135920.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135920 - SH0163 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0046 - - - Common Name - Shigella flexneri - - - Strain - IB0046 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033377 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135921.xml b/t/data/st_api_lims_new/st/samples/1135921.xml deleted file mode 100644 index 8b22dc31..00000000 --- a/t/data/st_api_lims_new/st/samples/1135921.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135921 - SH0164 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0047 - - - Common Name - Shigella flexneri - - - Strain - IB0047 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033378 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135922.xml b/t/data/st_api_lims_new/st/samples/1135922.xml deleted file mode 100644 index fe966831..00000000 --- a/t/data/st_api_lims_new/st/samples/1135922.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135922 - SH0165 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0068 - - - Common Name - Shigella flexneri - - - Strain - IB0068 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033379 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135923.xml b/t/data/st_api_lims_new/st/samples/1135923.xml deleted file mode 100644 index c4b79172..00000000 --- a/t/data/st_api_lims_new/st/samples/1135923.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135923 - SH0166 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1716 - - - Common Name - Shigella flexneri - - - Strain - IB1716 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033380 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135924.xml b/t/data/st_api_lims_new/st/samples/1135924.xml deleted file mode 100644 index 01006ac7..00000000 --- a/t/data/st_api_lims_new/st/samples/1135924.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135924 - SH0167 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1753 - - - Common Name - Shigella flexneri - - - Strain - IB1753 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033381 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135925.xml b/t/data/st_api_lims_new/st/samples/1135925.xml deleted file mode 100644 index 1aeb03f6..00000000 --- a/t/data/st_api_lims_new/st/samples/1135925.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135925 - SH0168 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1757 - - - Common Name - Shigella flexneri - - - Strain - IB1757 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033382 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135926.xml b/t/data/st_api_lims_new/st/samples/1135926.xml deleted file mode 100644 index 57ec6dc0..00000000 --- a/t/data/st_api_lims_new/st/samples/1135926.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135926 - SH0169 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1762 - - - Common Name - Shigella flexneri - - - Strain - IB1762 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033383 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135927.xml b/t/data/st_api_lims_new/st/samples/1135927.xml deleted file mode 100644 index 98af4a94..00000000 --- a/t/data/st_api_lims_new/st/samples/1135927.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135927 - SH0170 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1773 - - - Common Name - Shigella flexneri - - - Strain - IB1773 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033384 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135928.xml b/t/data/st_api_lims_new/st/samples/1135928.xml deleted file mode 100644 index 70fb3405..00000000 --- a/t/data/st_api_lims_new/st/samples/1135928.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135928 - SH0171 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB4229 - - - Common Name - Shigella flexneri - - - Strain - IB4229 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033385 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135929.xml b/t/data/st_api_lims_new/st/samples/1135929.xml deleted file mode 100644 index fd2fd3be..00000000 --- a/t/data/st_api_lims_new/st/samples/1135929.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135929 - SH0172 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB1743 - - - Common Name - Shigella flexneri - - - Strain - IB1743 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033386 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135930.xml b/t/data/st_api_lims_new/st/samples/1135930.xml deleted file mode 100644 index e29e99db..00000000 --- a/t/data/st_api_lims_new/st/samples/1135930.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135930 - SH0173 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - M90T - - - Common Name - Shigella flexneri - - - Strain - M90T - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033387 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135931.xml b/t/data/st_api_lims_new/st/samples/1135931.xml deleted file mode 100644 index a3bdb505..00000000 --- a/t/data/st_api_lims_new/st/samples/1135931.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135931 - SH0174 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - YSH6000 - - - Common Name - Shigella flexneri - - - Strain - YSH6000 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033388 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135932.xml b/t/data/st_api_lims_new/st/samples/1135932.xml deleted file mode 100644 index 8e2fb5d5..00000000 --- a/t/data/st_api_lims_new/st/samples/1135932.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135932 - SH0175 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB3325 - - - Common Name - Shigella flexneri - - - Strain - IB3325 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033389 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135933.xml b/t/data/st_api_lims_new/st/samples/1135933.xml deleted file mode 100644 index f88d3bbf..00000000 --- a/t/data/st_api_lims_new/st/samples/1135933.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135933 - SH0176 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0058 - - - Common Name - Shigella flexneri - - - Strain - IB0058 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033390 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1135934.xml b/t/data/st_api_lims_new/st/samples/1135934.xml deleted file mode 100644 index 9ddf810b..00000000 --- a/t/data/st_api_lims_new/st/samples/1135934.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1135934 - SH0177 - 1826 - false - - - Organism - Shigella flexneri - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - IB0064 - - - Common Name - Shigella flexneri - - - Strain - IB0064 - - - TAXON ID - 623 - - - ENA Sample Accession Number - ERS033391 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 1826 - diff --git a/t/data/st_api_lims_new/st/samples/1139014.xml b/t/data/st_api_lims_new/st/samples/1139014.xml deleted file mode 100644 index 7180fdef..00000000 --- a/t/data/st_api_lims_new/st/samples/1139014.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139014 - SPN742 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 742 - - - Common Name - Streptococcus pneumoniae - - - Strain - 742 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069340 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139015.xml b/t/data/st_api_lims_new/st/samples/1139015.xml deleted file mode 100644 index bc21923a..00000000 --- a/t/data/st_api_lims_new/st/samples/1139015.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139015 - SPN726 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 726 - - - Common Name - Streptococcus pneumoniae - - - Strain - 726 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069341 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139016.xml b/t/data/st_api_lims_new/st/samples/1139016.xml deleted file mode 100644 index 82940047..00000000 --- a/t/data/st_api_lims_new/st/samples/1139016.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139016 - SPN792 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 792 - - - Common Name - Streptococcus pneumoniae - - - Strain - 792 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069342 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139017.xml b/t/data/st_api_lims_new/st/samples/1139017.xml deleted file mode 100644 index 1d0f4f7b..00000000 --- a/t/data/st_api_lims_new/st/samples/1139017.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139017 - SPN772 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 772 - - - Common Name - Streptococcus pneumoniae - - - Strain - 772 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069343 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139018.xml b/t/data/st_api_lims_new/st/samples/1139018.xml deleted file mode 100644 index 12644f35..00000000 --- a/t/data/st_api_lims_new/st/samples/1139018.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139018 - SPN3402 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 3402 - - - Common Name - Streptococcus pneumoniae - - - Strain - 3402 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069344 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139019.xml b/t/data/st_api_lims_new/st/samples/1139019.xml deleted file mode 100644 index 8e95ff53..00000000 --- a/t/data/st_api_lims_new/st/samples/1139019.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139019 - SPN1110 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 1110 - - - Common Name - Streptococcus pneumoniae - - - Strain - 1110 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069345 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139020.xml b/t/data/st_api_lims_new/st/samples/1139020.xml deleted file mode 100644 index b4692a48..00000000 --- a/t/data/st_api_lims_new/st/samples/1139020.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139020 - SPN8206 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 8206 - - - Common Name - Streptococcus pneumoniae - - - Strain - 8206 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069346 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139021.xml b/t/data/st_api_lims_new/st/samples/1139021.xml deleted file mode 100644 index 4cc4d89e..00000000 --- a/t/data/st_api_lims_new/st/samples/1139021.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139021 - SPN5441 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 5441 - - - Common Name - Streptococcus pneumoniae - - - Strain - 5441 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069347 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139022.xml b/t/data/st_api_lims_new/st/samples/1139022.xml deleted file mode 100644 index 58797c2e..00000000 --- a/t/data/st_api_lims_new/st/samples/1139022.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139022 - SPN456 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 456 - - - Common Name - Streptococcus pneumoniae - - - Strain - 456 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069348 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139023.xml b/t/data/st_api_lims_new/st/samples/1139023.xml deleted file mode 100644 index 8b8e0907..00000000 --- a/t/data/st_api_lims_new/st/samples/1139023.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139023 - SPN485 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - 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- - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139025.xml b/t/data/st_api_lims_new/st/samples/1139025.xml deleted file mode 100644 index 769a8459..00000000 --- a/t/data/st_api_lims_new/st/samples/1139025.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139025 - SPN4705 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 4705 - - - Common Name - Streptococcus pneumoniae - - - Strain - 4705 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069351 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139026.xml b/t/data/st_api_lims_new/st/samples/1139026.xml deleted file mode 100644 index 593c6ce6..00000000 --- a/t/data/st_api_lims_new/st/samples/1139026.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139026 - SPN9180 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 9180 - - - Common Name - Streptococcus pneumoniae - - - Strain - 9180 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069352 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139027.xml b/t/data/st_api_lims_new/st/samples/1139027.xml deleted file mode 100644 index 21f656d6..00000000 --- a/t/data/st_api_lims_new/st/samples/1139027.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139027 - SPN9188 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 9188 - - - Common Name - Streptococcus pneumoniae - - - Strain - 9188 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069353 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139028.xml b/t/data/st_api_lims_new/st/samples/1139028.xml deleted file mode 100644 index 49a9fbb0..00000000 --- a/t/data/st_api_lims_new/st/samples/1139028.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139028 - SPN9193 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 9193 - - - Common Name - Streptococcus pneumoniae - - - Strain - 9193 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069354 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - 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- - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139030.xml b/t/data/st_api_lims_new/st/samples/1139030.xml deleted file mode 100644 index b28b9d06..00000000 --- a/t/data/st_api_lims_new/st/samples/1139030.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139030 - SPN9404 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 9404 - - - Common Name - Streptococcus pneumoniae - - - Strain - 9404 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069356 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139031.xml b/t/data/st_api_lims_new/st/samples/1139031.xml deleted file mode 100644 index 44f129f1..00000000 --- a/t/data/st_api_lims_new/st/samples/1139031.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139031 - SPN9424 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 9424 - - - Common Name - Streptococcus pneumoniae - - - Strain - 9424 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069357 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139032.xml b/t/data/st_api_lims_new/st/samples/1139032.xml deleted file mode 100644 index 46ca9d38..00000000 --- a/t/data/st_api_lims_new/st/samples/1139032.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139032 - SPN9671 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 9671 - - - Common Name - Streptococcus pneumoniae - - - Strain - 9671 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069358 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 664 - diff --git a/t/data/st_api_lims_new/st/samples/1139033.xml b/t/data/st_api_lims_new/st/samples/1139033.xml deleted file mode 100644 index d48bdac2..00000000 --- a/t/data/st_api_lims_new/st/samples/1139033.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1139033 - SPN11864 - 664 - false - - - Organism - Streptococcus pneumoniae - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 11864 - - - Common Name - Streptococcus pneumoniae - - - Strain - 11864 - - - TAXON ID - 1313 - - - ENA Sample Accession Number - ERS069359 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - 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N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Activin - - - Dose - 10 ng/ml - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - Activin - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - Activin - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672015.xml b/t/data/st_api_lims_new/st/samples/1672015.xml deleted file mode 100644 index fc0a397f..00000000 --- a/t/data/st_api_lims_new/st/samples/1672015.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672015 - ACT-1-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - 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- - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Activin - - - Dose - 10 ng/ml - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - Activin - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - Activin - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672017.xml b/t/data/st_api_lims_new/st/samples/1672017.xml deleted file mode 100644 index 9a028605..00000000 --- a/t/data/st_api_lims_new/st/samples/1672017.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672017 - ACT-3-K27 - 2712 - false - - - Organism - 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N/A - - - Compound - Activin - - - Dose - 10 ng/ml - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - Activin - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - Activin - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672018.xml b/t/data/st_api_lims_new/st/samples/1672018.xml deleted file mode 100644 index 56128f7c..00000000 --- a/t/data/st_api_lims_new/st/samples/1672018.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672018 - SB-1-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_H3K4me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329833 - - - Sample Description - ChIP for H3K4me3 from H9 cells treated with 10uM SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672019.xml b/t/data/st_api_lims_new/st/samples/1672019.xml deleted file mode 100644 index 4b123493..00000000 --- a/t/data/st_api_lims_new/st/samples/1672019.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672019 - SB-2-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_H3K4me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329834 - - - Sample Description - ChIP for H3K4me3 from H9 cells treated with 10uM SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672020.xml b/t/data/st_api_lims_new/st/samples/1672020.xml deleted file mode 100644 index a47cc4f7..00000000 --- a/t/data/st_api_lims_new/st/samples/1672020.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672020 - SB-3-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_H3K4me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329835 - - - Sample Description - ChIP for H3K4me3 from H9 cells treated with 10uM SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672021.xml b/t/data/st_api_lims_new/st/samples/1672021.xml deleted file mode 100644 index 2458355b..00000000 --- a/t/data/st_api_lims_new/st/samples/1672021.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672021 - SB-1-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_H3K27me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329836 - - - Sample Description - ChIP for H3K4me27 from H9 cells treated with 10uM SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672022.xml b/t/data/st_api_lims_new/st/samples/1672022.xml deleted file mode 100644 index 80f7c9c0..00000000 --- a/t/data/st_api_lims_new/st/samples/1672022.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672022 - SB-2-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_H3K27me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329837 - - - Sample Description - ChIP for H3K4me27 from H9 cells treated with 10uM SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672023.xml b/t/data/st_api_lims_new/st/samples/1672023.xml deleted file mode 100644 index a755c4ef..00000000 --- a/t/data/st_api_lims_new/st/samples/1672023.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672023 - SB-3-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_H3K27me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329838 - - - Sample Description - ChIP for H3K4me27 from H9 cells treated with 10uM SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - 4h - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672024.xml b/t/data/st_api_lims_new/st/samples/1672024.xml deleted file mode 100644 index 037d56e4..00000000 --- a/t/data/st_api_lims_new/st/samples/1672024.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672024 - SCRD-1-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Dpy30_H3K4me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329839 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing a control shRNA matched with the Dpy30 KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672025.xml b/t/data/st_api_lims_new/st/samples/1672025.xml deleted file mode 100644 index 84be88c0..00000000 --- a/t/data/st_api_lims_new/st/samples/1672025.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672025 - SCRD-2-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Dpy30_H3K4me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329840 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing a control shRNA matched with the Dpy30 KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672026.xml b/t/data/st_api_lims_new/st/samples/1672026.xml deleted file mode 100644 index 5e49a3bd..00000000 --- a/t/data/st_api_lims_new/st/samples/1672026.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672026 - SCRD-3-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Dpy30_H3K4me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329841 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing a control shRNA matched with the Dpy30 KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - 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- - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672028.xml b/t/data/st_api_lims_new/st/samples/1672028.xml deleted file mode 100644 index f871aae2..00000000 --- a/t/data/st_api_lims_new/st/samples/1672028.xml +++ /dev/null @@ -1,227 +0,0 @@ - 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N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672029.xml b/t/data/st_api_lims_new/st/samples/1672029.xml deleted file mode 100644 index 307be7fc..00000000 --- a/t/data/st_api_lims_new/st/samples/1672029.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672029 - SCRD-3-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Dpy30_H3K27me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329844 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing a control shRNA matched with the Dpy30 KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - 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Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Dpy30 shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672031.xml b/t/data/st_api_lims_new/st/samples/1672031.xml deleted file mode 100644 index f09fa801..00000000 --- a/t/data/st_api_lims_new/st/samples/1672031.xml +++ /dev/null @@ -1,227 +0,0 @@ - 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N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672032.xml b/t/data/st_api_lims_new/st/samples/1672032.xml deleted file mode 100644 index 20d060f2..00000000 --- a/t/data/st_api_lims_new/st/samples/1672032.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672032 - DPY-3-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Dpy30 KD_H3K4me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329847 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing an shRNA against Dpy30 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Dpy30 shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672033.xml b/t/data/st_api_lims_new/st/samples/1672033.xml deleted file mode 100644 index 56d9213b..00000000 --- a/t/data/st_api_lims_new/st/samples/1672033.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672033 - DPY-1-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Dpy30 KD_H3K27me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329848 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing an shRNA against Dpy30 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Dpy30 shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672034.xml b/t/data/st_api_lims_new/st/samples/1672034.xml deleted file mode 100644 index ea283d24..00000000 --- a/t/data/st_api_lims_new/st/samples/1672034.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672034 - DPY-2-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Dpy30 KD_H3K27me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329849 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing an shRNA against Dpy30 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Dpy30 shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672035.xml b/t/data/st_api_lims_new/st/samples/1672035.xml deleted file mode 100644 index 0b7bfcc9..00000000 --- a/t/data/st_api_lims_new/st/samples/1672035.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672035 - DPY-3-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Dpy30 KD_H3K27me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329850 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing an shRNA against Dpy30 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Dpy30 shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672036.xml b/t/data/st_api_lims_new/st/samples/1672036.xml deleted file mode 100644 index dd076225..00000000 --- a/t/data/st_api_lims_new/st/samples/1672036.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672036 - SCRN-1-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Nanog_H3K4me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329851 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing a control shRNA matched with the Nanog KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672037.xml b/t/data/st_api_lims_new/st/samples/1672037.xml deleted file mode 100644 index d02254f4..00000000 --- a/t/data/st_api_lims_new/st/samples/1672037.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672037 - SCRN-2-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Nanog_H3K4me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329852 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing a control shRNA matched with the Nanog KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672038.xml b/t/data/st_api_lims_new/st/samples/1672038.xml deleted file mode 100644 index 7d8f5428..00000000 --- a/t/data/st_api_lims_new/st/samples/1672038.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672038 - SCRN-3-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Nanog_H3K4me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329853 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing a control shRNA matched with the Nanog KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672039.xml b/t/data/st_api_lims_new/st/samples/1672039.xml deleted file mode 100644 index fe90d15e..00000000 --- a/t/data/st_api_lims_new/st/samples/1672039.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672039 - SCRN-1-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Nanog_H3K27me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329854 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing a control shRNA matched with the Nanog KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672040.xml b/t/data/st_api_lims_new/st/samples/1672040.xml deleted file mode 100644 index caf628eb..00000000 --- a/t/data/st_api_lims_new/st/samples/1672040.xml +++ /dev/null @@ -1,227 +0,0 @@ - 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N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672041.xml b/t/data/st_api_lims_new/st/samples/1672041.xml deleted file mode 100644 index 26a608a2..00000000 --- a/t/data/st_api_lims_new/st/samples/1672041.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672041 - SCRN-3-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Scramble control Nanog_H3K27me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329856 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing a control shRNA matched with the Nanog KD lines - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Scramble shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672042.xml b/t/data/st_api_lims_new/st/samples/1672042.xml deleted file mode 100644 index 56150b08..00000000 --- a/t/data/st_api_lims_new/st/samples/1672042.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672042 - NAN-1-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_H3K4me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329857 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672043.xml b/t/data/st_api_lims_new/st/samples/1672043.xml deleted file mode 100644 index fbce8879..00000000 --- a/t/data/st_api_lims_new/st/samples/1672043.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672043 - NAN-2-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_H3K4me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329858 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672044.xml b/t/data/st_api_lims_new/st/samples/1672044.xml deleted file mode 100644 index d33666d7..00000000 --- a/t/data/st_api_lims_new/st/samples/1672044.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672044 - NAN-3-K4 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_H3K4me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329859 - - - Sample Description - ChIP for H3K4me3 from H9 cells expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K4me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672045.xml b/t/data/st_api_lims_new/st/samples/1672045.xml deleted file mode 100644 index aa02d5f5..00000000 --- a/t/data/st_api_lims_new/st/samples/1672045.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672045 - NAN-1-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_H3K27me3_replicate1 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329860 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672046.xml b/t/data/st_api_lims_new/st/samples/1672046.xml deleted file mode 100644 index 5d3f40f4..00000000 --- a/t/data/st_api_lims_new/st/samples/1672046.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672046 - NAN-2-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_H3K27me3_replicate2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329861 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672047.xml b/t/data/st_api_lims_new/st/samples/1672047.xml deleted file mode 100644 index b4b1e24a..00000000 --- a/t/data/st_api_lims_new/st/samples/1672047.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672047 - NAN-3-K27 - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_H3K27me3_replicate3 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329862 - - - Sample Description - ChIP for H3K4me27 from H9 cells expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - Anti H3K27me3 - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672048.xml b/t/data/st_api_lims_new/st/samples/1672048.xml deleted file mode 100644 index 5fb49bfe..00000000 --- a/t/data/st_api_lims_new/st/samples/1672048.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672048 - ACT-INPUT - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Activin_Input - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329863 - - - Sample Description - Pooled input DNA for ChIPs in normal and control shRNA expressing H9 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Mixed wildtype/Scramble shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Activin - - - Dose - 10 ng/ml - - - Immunoprecipitate - None - - - Growth Condition - Activin - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - Activin - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672049.xml b/t/data/st_api_lims_new/st/samples/1672049.xml deleted file mode 100644 index 141662a1..00000000 --- a/t/data/st_api_lims_new/st/samples/1672049.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672049 - SB-INPUT - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - SB_Input - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329864 - - - Sample Description - Pooled input DNA for ChIPs in H9 treated with SB431542 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - SB431542 - - - Dose - 10 uM - - - Immunoprecipitate - None - - - Growth Condition - SB431542 - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - SB431542 - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672050.xml b/t/data/st_api_lims_new/st/samples/1672050.xml deleted file mode 100644 index 4c53a750..00000000 --- a/t/data/st_api_lims_new/st/samples/1672050.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672050 - DPY-INPUT - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Dpy30 KD_input - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329865 - - - Sample Description - Pooled input DNA for ChIPs in H9 expressing an shRNA against Dpy30 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Dpy30 shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Dpy30 shRNA - - - Dose - N/A - - - Immunoprecipitate - None - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1672051.xml b/t/data/st_api_lims_new/st/samples/1672051.xml deleted file mode 100644 index 83cf9277..00000000 --- a/t/data/st_api_lims_new/st/samples/1672051.xml +++ /dev/null @@ -1,227 +0,0 @@ - - - 1672051 - NAN-INPUT - 2712 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 25 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Female - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Nanog KD_input - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - ERS329866 - - - Sample Description - Pooled input DNA for ChIPs in H9 expressing an shRNA against Nanog - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Nanog shRNA - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - H9 hESC line - - - Disease State - N/A - - - Compound - Nanog shRNA - - - Dose - N/A - - - Immunoprecipitate - None - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - - - - - - - - - - - - - - - - - - - - - 2712 - diff --git a/t/data/st_api_lims_new/st/samples/1673265.xml b/t/data/st_api_lims_new/st/samples/1673265.xml deleted file mode 100644 index abe299ea..00000000 --- a/t/data/st_api_lims_new/st/samples/1673265.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1673265 - k-1 - 2717 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - - - - DNA source - Genomic - - - Public Name - k-1 - - - Common Name - mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS331837 - - - Sample Description - Enriched mRNA from ES cells. A 5 base indexing sequence (GAGGC) is bases 6 to 10 of read 1 followed by polyT - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - ES Cell - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - control - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38) - - - - - - - - - - 2717 - diff --git a/t/data/st_api_lims_new/st/samples/1673266.xml b/t/data/st_api_lims_new/st/samples/1673266.xml deleted file mode 100644 index 54392037..00000000 --- a/t/data/st_api_lims_new/st/samples/1673266.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1673266 - k-2 - 2717 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - - - - DNA source - Genomic - - - Public Name - k-2 - - - Common Name - mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS331838 - - - Sample Description - Enriched mRNA from ES cells. A 5 base indexing sequence (AGAAG) is bases 6 to 10 of read 1 followed by polyT - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - ES Cell - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - control - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38) - - - - - - - - - - 2717 - diff --git a/t/data/st_api_lims_new/st/samples/1673267.xml b/t/data/st_api_lims_new/st/samples/1673267.xml deleted file mode 100644 index dc63c81f..00000000 --- a/t/data/st_api_lims_new/st/samples/1673267.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1673267 - k-3 - 2717 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - - - - DNA source - Genomic - - - Public Name - k-3 - - - Common Name - mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS331839 - - - Sample Description - Enriched mRNA from ES cells. A 5 base indexing sequence (CAGAG) is bases 6 to 10 of read 1 followed by polyT - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - ES Cell - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - control - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38) - - - - - - - - - - 2717 - diff --git a/t/data/st_api_lims_new/st/samples/1673268.xml b/t/data/st_api_lims_new/st/samples/1673268.xml deleted file mode 100644 index 2d7bfda8..00000000 --- a/t/data/st_api_lims_new/st/samples/1673268.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1673268 - 2i-1 - 2717 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - - - - DNA source - Genomic - - - Public Name - 2i-1 - - - Common Name - mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS331840 - - - Sample Description - Enriched mRNA from ES cells. A 5 base indexing sequence (GCACG) is bases 6 to 10 of read 1 followed by polyT - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - ES Cell - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - 2i - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38) - - - - - - - - - - 2717 - diff --git a/t/data/st_api_lims_new/st/samples/1673269.xml b/t/data/st_api_lims_new/st/samples/1673269.xml deleted file mode 100644 index e9ba82d3..00000000 --- a/t/data/st_api_lims_new/st/samples/1673269.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1673269 - 2i-2 - 2717 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - - - - DNA source - Genomic - - - Public Name - 2i-2 - - - Common Name - mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS331841 - - - Sample Description - Enriched mRNA from ES cells. A 5 base indexing sequence (CGCAA) is bases 6 to 10 of read 1 followed by polyT - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - ES Cell - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - 2i - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38) - - - - - - - - - - 2717 - diff --git a/t/data/st_api_lims_new/st/samples/1673270.xml b/t/data/st_api_lims_new/st/samples/1673270.xml deleted file mode 100644 index 2dbc7b43..00000000 --- a/t/data/st_api_lims_new/st/samples/1673270.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1673270 - 2i-3 - 2717 - false - - - Organism - Mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - Donor Id - - - - DNA source - Genomic - - - Public Name - 2i-3 - - - Common Name - mus musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS331842 - - - Sample Description - Enriched mRNA from ES cells. A 5 base indexing sequence (CAAGA) is bases 6 to 10 of read 1 followed by polyT - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - Wildtype - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - ES Cell - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - 2i - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - N/A - - - Reference Genome - Mus_musculus (GRCm38) - - - - - - - - - - 2717 - diff --git a/t/data/st_api_lims_new/st/samples/1677420.xml b/t/data/st_api_lims_new/st/samples/1677420.xml deleted file mode 100644 index dcb8cef3..00000000 --- a/t/data/st_api_lims_new/st/samples/1677420.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1677420 - zmp_ph23_1m - 2311 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - - - - DNA source - Genomic - - - Public Name - ZMP phenotype 23.1 mutant - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS336311 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 23 clutch 1. A 5 base indexing sequence (GAGGCG) is bases 7 to 12 of non-index read 2 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph23 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching : Long pec - ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - 2311 - diff --git a/t/data/st_api_lims_new/st/samples/1677421.xml b/t/data/st_api_lims_new/st/samples/1677421.xml deleted file mode 100644 index 2bb85e2a..00000000 --- a/t/data/st_api_lims_new/st/samples/1677421.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1677421 - zmp_ph23_1s - 2311 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - - - - DNA source - Genomic - - - Public Name - ZMP phenotype 23.1 sibling - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS336312 - - - Sample Description - 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 23 clutch 1. A 5 base indexing sequence (AGAAGG) is bases 7 to 12 of non-index read 2 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph23 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching : Long pec - ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - 2311 - diff --git a/t/data/st_api_lims_new/st/samples/1677422.xml b/t/data/st_api_lims_new/st/samples/1677422.xml deleted file mode 100644 index a7e88ee0..00000000 --- a/t/data/st_api_lims_new/st/samples/1677422.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1677422 - zmp_ph23_2m - 2311 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - - - - DNA source - Genomic - - - Public Name - ZMP phenotype 23.2 mutant - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS336313 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 23 clutch 2. A 5 base indexing sequence (CAGAGG) is bases 7 to 12 of non-index read 2 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph23 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching : Long pec - ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - 2311 - diff --git a/t/data/st_api_lims_new/st/samples/1677423.xml b/t/data/st_api_lims_new/st/samples/1677423.xml deleted file mode 100644 index 0fe0ca01..00000000 --- a/t/data/st_api_lims_new/st/samples/1677423.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1677423 - zmp_ph23_2s - 2311 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - - - - DNA source - Genomic - - - Public Name - ZMP phenotype 23.2 sibling - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS336314 - - - Sample Description - 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 23 clutch 2. A 5 base indexing sequence (GCACGG) is bases 7 to 12 of non-index read 2 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph23 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching : Long pec - ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - 2311 - diff --git a/t/data/st_api_lims_new/st/samples/1677424.xml b/t/data/st_api_lims_new/st/samples/1677424.xml deleted file mode 100644 index b2b71dba..00000000 --- a/t/data/st_api_lims_new/st/samples/1677424.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1677424 - zmp_ph23_3m - 2311 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - - - - DNA source - Genomic - - - Public Name - ZMP phenotype 23.3 mutant - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS336315 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from ZMP phenotype 23 clutch 3. A 5 base indexing sequence (CGCAAG) is bases 7 to 12 of non-index read 2 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph23 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching : Long pec - ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - 2311 - diff --git a/t/data/st_api_lims_new/st/samples/1677425.xml b/t/data/st_api_lims_new/st/samples/1677425.xml deleted file mode 100644 index e1d7d819..00000000 --- a/t/data/st_api_lims_new/st/samples/1677425.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1677425 - zmp_ph23_3s - 2311 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - - - - DNA source - Genomic - - - Public Name - ZMP phenotype 23.3 sibling - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS336316 - - - Sample Description - 3' end enriched mRNA from morphologically normal sibling embryos from ZMP phenotype 23 clutch 3. A 6 base indexing sequence (CAAGAG) is bases 7 to 12 of non-index read 2 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_ph23 - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching : Long pec - ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - 2311 - diff --git a/t/data/st_api_lims_new/st/samples/1678317.xml b/t/data/st_api_lims_new/st/samples/1678317.xml deleted file mode 100644 index 23c3d478..00000000 --- a/t/data/st_api_lims_new/st/samples/1678317.xml +++ /dev/null @@ -1,214 +0,0 @@ - - - 1678317 - PD12856a_pd - 2687 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD12856a - - - DNA source - Genomic - - - Public Name - PD12856a - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001170543 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Melanoma - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 2687 - diff --git a/t/data/st_api_lims_new/st/samples/1678318.xml b/t/data/st_api_lims_new/st/samples/1678318.xml deleted file mode 100644 index d4b3c876..00000000 --- a/t/data/st_api_lims_new/st/samples/1678318.xml +++ /dev/null @@ -1,214 +0,0 @@ - - - 1678318 - PD12856c_pd - 2687 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD12856c - - - DNA source - Genomic - - - Public Name - PD12856c - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001170544 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Melanoma - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 2687 - diff --git a/t/data/st_api_lims_new/st/samples/1678319.xml b/t/data/st_api_lims_new/st/samples/1678319.xml deleted file mode 100644 index 19d4f726..00000000 --- a/t/data/st_api_lims_new/st/samples/1678319.xml +++ /dev/null @@ -1,214 +0,0 @@ - - - 1678319 - PD13314a_pd - 2687 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD13314a - - - DNA source - Genomic - - - Public Name - PD13314a - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001170545 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Melanoma - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 2687 - diff --git a/t/data/st_api_lims_new/st/samples/1678320.xml b/t/data/st_api_lims_new/st/samples/1678320.xml deleted file mode 100644 index 32d996bc..00000000 --- a/t/data/st_api_lims_new/st/samples/1678320.xml +++ /dev/null @@ -1,214 +0,0 @@ - - - 1678320 - PD13314c_pd - 2687 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD13314c - - - DNA source - Genomic - - - Public Name - PD13314c - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001170546 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Melanoma - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 2687 - diff --git a/t/data/st_api_lims_new/st/samples/1678321.xml b/t/data/st_api_lims_new/st/samples/1678321.xml deleted file mode 100644 index 90ccd1d6..00000000 --- a/t/data/st_api_lims_new/st/samples/1678321.xml +++ /dev/null @@ -1,214 +0,0 @@ - - - 1678321 - PD12856b_pd - 2687 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD12856b - - - DNA source - Genomic - - - Public Name - PD12856b - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001170547 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Normal - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 2687 - diff --git a/t/data/st_api_lims_new/st/samples/1678322.xml b/t/data/st_api_lims_new/st/samples/1678322.xml deleted file mode 100644 index 6a57eee8..00000000 --- a/t/data/st_api_lims_new/st/samples/1678322.xml +++ /dev/null @@ -1,214 +0,0 @@ - - - 1678322 - PD13314b2_pd - 2687 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - Donor Id - PD13314b2 - - - DNA source - Genomic - - - Public Name - PD13314b2 - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001170548 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Normal - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 2687 - diff --git a/t/data/st_api_lims_new/st/samples/1750.xml b/t/data/st_api_lims_new/st/samples/1750.xml deleted file mode 100644 index 012ebca1..00000000 --- a/t/data/st_api_lims_new/st/samples/1750.xml +++ /dev/null @@ -1,209 +0,0 @@ - - - 1750 - p242-NspI-PCR 2A2 - 667 - - - Phenotype - - - - Sample purified - - - - TAXON ID - 7955 - - - Country of origin - - - - Treatment - - - - Time Point - - - - Date of sample extraction - - - - Sample Description - AB GO (grandmother) of the MGH meiotic cross. The same DNA was split into three aliquots (of which this is reaction A), processed in parallel, they were: NspI cut, ligated with modified recuttable adaptor (ATTATGAGCACGACAGACGCCTGATCTRCATG and YAGATCAGGCGTCTGTCGTGCTCATAA), and PCR amplified. - - - - ENA Sample Accession Number - ERS015522 - - - Common Name - Danio rerio - - - Gender - - - - Mother - - - - Ethnicity - - - - Compound - - - - Cell Type - - - - Age - - - - Genotype - - - - Volume (µl) - - - - Dose - - - - Organism Part - - - - Growth Condition - - - - Concentration - - - - Public Name - MGH cross, AB G0, NspI digest (A), 400-600 - - - Subject - - - - RNAi - - - - Concentration determind by - - - - Is re-submitted? - - - - DNA source - - - - Sample extraction method - - - - Disease - - - - Sibling - - - - Strain - AB (MGH) - - - Cohort - - - - Immunoprecipitate - - - - Disease State - - - - Sample storage conditions - - - - Sample type - - - - Date of sample collection - - - - Developmental Stage - - - - Purification method - - - - Sample Visibility - Hold - - - GC content - Neutral - - - Father - - - - Plate - - - - Geographical region - - - - Replicate - - - - Organism - Danio rerio - - - Reference Genome - - - - - - - - - - - 667 - diff --git a/t/data/st_api_lims_new/st/samples/345259.xml b/t/data/st_api_lims_new/st/samples/345259.xml deleted file mode 100644 index a646c5a2..00000000 --- a/t/data/st_api_lims_new/st/samples/345259.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 345259 - WTCCC174444 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - Human - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001023865 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Northern - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo sapiens - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/345353.xml b/t/data/st_api_lims_new/st/samples/345353.xml deleted file mode 100644 index 798a6512..00000000 --- a/t/data/st_api_lims_new/st/samples/345353.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 345353 - WTCCC174538 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - Human - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001023959 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Northern - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo sapiens - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/345384.xml b/t/data/st_api_lims_new/st/samples/345384.xml deleted file mode 100644 index a4cbbf20..00000000 --- a/t/data/st_api_lims_new/st/samples/345384.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 345384 - WTCCC174569 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - Human - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001023990 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Northern - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo sapiens - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/345394.xml b/t/data/st_api_lims_new/st/samples/345394.xml deleted file mode 100644 index caef836c..00000000 --- a/t/data/st_api_lims_new/st/samples/345394.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 345394 - WTCCC174579 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - Hold - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - Human - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001024000 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Northern - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo sapiens - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/351073.xml b/t/data/st_api_lims_new/st/samples/351073.xml deleted file mode 100644 index 7eaf568b..00000000 --- a/t/data/st_api_lims_new/st/samples/351073.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 351073 - WTCCC125541 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - - - - Public Name - - - - Gender - Male - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001072032 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Scotland - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo Sapien - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/351081.xml b/t/data/st_api_lims_new/st/samples/351081.xml deleted file mode 100644 index 00f2870b..00000000 --- a/t/data/st_api_lims_new/st/samples/351081.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 351081 - WTCCC125549 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001072035 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Scotland - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo Sapien - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/351089.xml b/t/data/st_api_lims_new/st/samples/351089.xml deleted file mode 100644 index e887dd50..00000000 --- a/t/data/st_api_lims_new/st/samples/351089.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 351089 - WTCCC125557 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001072036 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Scotland - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo Sapien - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/351099.xml b/t/data/st_api_lims_new/st/samples/351099.xml deleted file mode 100644 index 7e219db1..00000000 --- a/t/data/st_api_lims_new/st/samples/351099.xml +++ /dev/null @@ -1,223 +0,0 @@ - - - 351099 - WTCCC125567 - 747 - false - - - Treatment - - - - Time Point - - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - UK - - - Concentration - - - - DNA source - - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - - - - Public Name - - - - Gender - Female - - - Volume (µl) - - - - Developmental Stage - - - - Plate - - - - Ethnicity - unknown - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - EGAN00001072037 - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - Scotland - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - WTCCC - - - Age - - - - Sample Description - - - - Common Name - Homo Sapien - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 747 - diff --git a/t/data/st_api_lims_new/st/samples/7283.xml b/t/data/st_api_lims_new/st/samples/7283.xml deleted file mode 100644 index 8e6af97a..00000000 --- a/t/data/st_api_lims_new/st/samples/7283.xml +++ /dev/null @@ -1,266 +0,0 @@ - - - 7283 - PD3918a - 333 - - - Phenotype - - - - Sample purified - - - - TAXON ID - 9606 - - - Country of origin - - - - Treatment - - - - Time Point - - - - Date of sample extraction - - - - Sample Description - - - - ENA Sample Accession Number - EGAN00001001569 - - - Common Name - Homo sapiens - - - Gender - Male - - - Mother - - - - Ethnicity - - - - Compound - - - - Cell Type - - - - Age - - - - Genotype - - - - Volume (µl) - - - - Dose - - - - Organism Part - - - - Growth Condition - - - - Concentration - - - - Public Name - - - - Subject - - - - RNAi - - - - Concentration determind by - - - - Is re-submitted? - - - - DNA source - Genomic - - - Sample extraction method - - - - Disease - - - - Sibling - - - - Strain - - - - Cohort - - - - Immunoprecipitate - - - - Disease State - - - - Sample storage conditions - - - - Sample type - - - - Date of sample collection - - - - Developmental Stage - - - - Purification method - - - - Sample Visibility - Hold - - - GC content - Neutral - - - Father - - - - Plate - - - - Geographical region - - - - Replicate - - - - Organism - Human - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 333 - diff --git a/t/data/st_api_lims_new/st/studies/11.xml b/t/data/st_api_lims_new/st/studies/11.xml deleted file mode 100644 index 344808af..00000000 --- a/t/data/st_api_lims_new/st/studies/11.xml +++ /dev/null @@ -1,165 +0,0 @@ - - - 11 - Trypanosoma brucei - false - 45 - - - jm15 - jm15@sanger.ac.uk - Jacqueline McQuillan - 67 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - parkhill - parkhill@sanger.ac.uk - Julian Parkhill - 45 - - - - - 2007-10-29 21:25:58 +0000 - 2009-11-05 16:00:02 +0000 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - - - - Policy - - - - Study description - Pathogen. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - - - - ENA Study Accession Number - - - - Title - - - - Abstract - - - - ENA Project ID - - - - Study Type - Not specified - - - Faculty Sponsor - Julian Parkhill - - - What sort of study is this? - not specified - - - Reference Genome - dodo - - - diff --git a/t/data/st_api_lims_new/st/studies/162.xml b/t/data/st_api_lims_new/st/studies/162.xml deleted file mode 100644 index 97bb5f58..00000000 --- a/t/data/st_api_lims_new/st/studies/162.xml +++ /dev/null @@ -1,196 +0,0 @@ - - - 162 - Chlamydia trachomatis global diversity project - true - 112 - - - chc - chc@sanger.ac.uk - Craig Corton - 101 - - - sh16 - sh16@sanger.ac.uk - Simon Harris - 155 - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - hss - hss@sanger.ac.uk - Helena Seth-Smith - 229 - - - - - chc - chc@sanger.ac.uk - Craig Corton - 101 - - - jm15 - jm15@sanger.ac.uk - Jacqueline McQuillan - 67 - - - nds - nds@sanger.ac.uk - Nishadi De Silva - 383 - - - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - - - 2008-10-02 10:51:44 +0100 - 2010-09-10 13:32:17 +0100 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - standard - - - Policy - - - - Study description - Chlamydia trachomatis is the most common cause of sexually transmitted infections in the UK, a statistic which is also reflected globally. There are two biovariants of C. trachomatis: trachoma and lyphogranuloma venereum (LGV). Trachoma isolates are non-invasive, whereas the LGV strains are invasive causing a disseminating infection of the local draining lymph nodes. Genome analysis has shown that the ocular and the genital trachoma isolates are 99.6 % identical at the sequence level and only show small differences in overall gene content. However, differences in coding potential, and the loss of function through point mutation, have been used to subdivide the trachoma strains into those associated with ocular and genital infections. We have previously sequenced a two LGV isolates; a long-term laboratory passaged strain and the recent ‘epidemic’ clinical LGV isolate causing proctitis. From these strains it was evident that there were no whole gene differences and that the recent epidemic isolate was a classical LGV isolate and has been circulating in the human population for a long time: an old strain causing a new disease. We have now put together a global collection of LGV isolates and are a sequencing them to determine the global phylogeny of this pathogen.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - Yes - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - open - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - No - - - ENA Study Accession Number - ERP000089 - - - Title - Chlamydia trachomatis global diversity project - - - Abstract - To sequence a global collection of Chlamydia trachomatis LGV isolates in order to determine the global phylogeny. - - - - ENA Project ID - 0 - - - Study Type - Whole Genome Sequencing - - - Faculty Sponsor - Julian Parkhill - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - diff --git a/t/data/st_api_lims_new/st/studies/1811.xml b/t/data/st_api_lims_new/st/studies/1811.xml deleted file mode 100644 index 7a1a61fe..00000000 --- a/t/data/st_api_lims_new/st/studies/1811.xml +++ /dev/null @@ -1,171 +0,0 @@ - - - 1811 - Schistosoma mansoni methylome - true - 143 - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - cb3 - cb3@sanger.ac.uk - Christine Burrows - 312 - - - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - - - neh - neh@sanger.ac.uk - Nancy Holroyd - 143 - - - - - 2011-04-11 12:51:38 +0100 - 2011-04-11 12:52:48 +0100 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - standard - - - Policy - - - - Study description - High throughput sequencing of different life cycle stages of Schistosoma mansoni to identify loci that are methylated and use the information to focus on regions of biological relevance related to development and control of disease. - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - open - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - No - - - ENA Study Accession Number - ERP000608 - - - Title - Schistosoma mansoni methylome - - - Abstract - High throughput illumina sequencing of Schistosoma mansoni genomic DNA to identify methylated regions of the genome. - - - ENA Project ID - 0 - - - Study Type - Epigenetics - - - Faculty Sponsor - Matt Berriman - - - What sort of study is this? - other sequencing-based assay - - - Reference Genome - Schistosoma_mansoni (20100601) - - - diff --git a/t/data/st_api_lims_new/st/studies/1833.xml b/t/data/st_api_lims_new/st/studies/1833.xml deleted file mode 100644 index ee3cc168..00000000 --- a/t/data/st_api_lims_new/st/studies/1833.xml +++ /dev/null @@ -1,190 +0,0 @@ - - - 1833 - SEQCAP_Whole_Genome_Sequencing_of_Crohns_Disease_Patients - true - 86 - - - ak6 - ak6@sanger.ac.uk - Anja Kolb-Kokocinski - 224 - - - jr17 - jr17@sanger.ac.uk - Joshua Randall - 600 - - - mercury - mercury-sequencescape@hgi-mercury.internal.sanger.ac.uk - Mercury Human Genetics Informatics Pipelines - 638 - - - - - sarah - sarah - Sarah Sims - 137 - - - - - dw2 - dw2@sanger.ac.uk - Danielle Walker - 86 - - - - - 2011-05-17 11:32:34 +0100 - 2011-05-19 11:55:10 +0100 - - - Comment regarding data release timing and approval - - - - What is the data release strategy for this study? - managed - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Title - Whole genome sequencing of Crohn's disease patients - - - SNP study ID - - - - Comment regarding prevention of data release and approval - - - - EGA DAC Accession Number - - - - ENA Study Accession Number - EGAS00001000065 - - - HMDMC approval number - - - - Will you be using WTSI's standard access agreement? - Yes - - - Do any of the samples in this study contain human DNA? - Yes - - - ENA Project ID - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - SNP parent study ID - - - - Alignments in BAM - true - - - Abstract - We propose to begin sequencing whole genomes from population CD samples in mid 2011, to be ramped up in the first year of the QQ. The aim is to identiy low frequency and rare variation which contributes to CD risk but is not easily detectable by GWAS. Thes sequences will be compared to UK10K and Cambridge BioResource controls. - - - Study description - Population based sequencing of whole genomes of Crohn's disease patients. - - - Policy - https://www.sanger.ac.uk/datasharing/ - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Reason for delaying release - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study Visibility - Hold - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Delay for - - - - How is the data release to be timed? - standard - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Study name abbreviation - SC_WGSC - - - Faculty Sponsor - Jeffrey Barrett - - - What sort of study is this? - genomic sequencing - - - Study Type - Whole Genome Sequencing - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - diff --git a/t/data/st_api_lims_new/st/studies/198.xml b/t/data/st_api_lims_new/st/studies/198.xml deleted file mode 100644 index 88cbe0f2..00000000 --- a/t/data/st_api_lims_new/st/studies/198.xml +++ /dev/null @@ -1,165 +0,0 @@ - - - 198 - Illumina Controls - true - 83 - - - pc10 - pc10@sanger.ac.uk - Paul Coupland - 194 - - - - - hps - hps@sanger.ac.uk - Harold Swerdlow - 83 - - - - - hps - hps@sanger.ac.uk - Harold Swerdlow - 83 - - - - - 2008-11-13 13:27:48 +0000 - 2009-03-09 12:22:26 +0000 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - - - - Policy - - - - Study description - None - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - - - - Study Visibility - - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - - - - ENA Study Accession Number - - - - Title - - - - Abstract - - - - ENA Project ID - - - - Study Type - Not specified - - - Faculty Sponsor - None - - - What sort of study is this? - not specified - - - Reference Genome - - - - diff --git a/t/data/st_api_lims_new/st/studies/2278.xml b/t/data/st_api_lims_new/st/studies/2278.xml deleted file mode 100644 index c885bbff..00000000 --- a/t/data/st_api_lims_new/st/studies/2278.xml +++ /dev/null @@ -1,172 +0,0 @@ - - - 2278 - SEQCAP_WGS_Human_Evolution_3 - true - 86 - - - dw2 - dw2@sanger.ac.uk - Danielle Walker - 86 - - - - - cts - cts@sanger.ac.uk - Christopher Tyler-Smith - 533 - - - - - 2012-07-10 16:16:30 +0100 - 2012-08-07 15:29:30 +0100 - - - Comment regarding data release timing and approval - - - - What is the data release strategy for this study? - managed - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Title - Human Evolution 3 - - - SNP study ID - - - - Comment regarding prevention of data release and approval - - - - EGA DAC Accession Number - - - - ENA Study Accession Number - EGAS00001000315 - - - HMDMC approval number - 12/055 - - - Will you be using WTSI's standard access agreement? - Yes - - - Do any of the samples in this study contain human DNA? - Yes - - - ENA Project ID - 0 - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - SNP parent study ID - - - - Alignments in BAM - true - - - Abstract - According to current models of human expansion out of Africa around 60,000 years ago, there was an early divergence between the ancestors of Australian Aborigines on the one hand and the ancestors of Asians, Europeans and most other non-Africans on the other. Australian Aborigines are therefore of particular importance for understanding these early events, and the subsequent history of this branch of humanity. The project will sequence the mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, to address these questions. - - - Study description - The mtDNA and Y chromosome of up to 15 Australian Aborigines, concentrating on individuals with indigenous lineages, will be sequenced using the standard whole-genome sequencing followed by filtering out of autosomal and X sequences, so that only mtDNA and the Y chromosome will be analysed and released. - - - Policy - The mtDNA and Y-chromosomal data will be submitted to EGA and are accessible under managed data access. Autosomal and X data must be filtered out and stored but not released. -https://www.sanger.ac.uk/datasharing/ - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Reason for delaying release - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study Visibility - Hold - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Delay for - - - - How is the data release to be timed? - standard - - - Does this study require the removal of X chromosome and autosome sequence? - Yes - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Study name abbreviation - SC_HE3 - - - Faculty Sponsor - Chris Tyler-Smith - - - What sort of study is this? - genomic sequencing - - - Study Type - Whole Genome Sequencing - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - - diff --git a/t/data/st_api_lims_new/st/studies/2693.xml b/t/data/st_api_lims_new/st/studies/2693.xml deleted file mode 100644 index 1d124757..00000000 --- a/t/data/st_api_lims_new/st/studies/2693.xml +++ /dev/null @@ -1,182 +0,0 @@ - - - 2693 - HiPSCI Pilot - true - 191 - - - ncb - ncb@sanger.ac.uk - Nathalie C Smerdon - 191 - - - - - jgb - jgb@sanger.ac.uk - Jose Garcia-Bernardo - 785 - - - - - 2013-07-10 09:31:38 +0100 - 2013-07-11 08:14:42 +0100 - - - Study description - HiPSCI Pilot - -This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - true - - - ENA Project ID - - - - Abstract - R&D Work for HiPSCI project - - - Title - HiPSCI - - - ENA Study Accession Number - - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - not applicable - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - never - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - data validity - - - Has this been approved? - Yes - - - Comment regarding prevention of data release and approval - Pilot - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Epigenetics - - - What sort of study is this? - genotyping or cytogenetics - - - Reference Genome - Homo_sapiens (GRCh37_53) - - - Faculty Sponsor - Richard Durbin - - - diff --git a/t/data/st_api_lims_new/st/studies/292.xml b/t/data/st_api_lims_new/st/studies/292.xml deleted file mode 100644 index 4c65fd8f..00000000 --- a/t/data/st_api_lims_new/st/studies/292.xml +++ /dev/null @@ -1,177 +0,0 @@ - - - 292 - WTCCC Exon Resequencing - true - 129 - - - kp5 - kp5@sanger.ac.uk - Kimmo Palin - 158 - - - tpy - tpy@sanger.ac.uk - Tsun-Po Yang - 269 - - - kb1 - kb1@sanger.ac.uk - Karen McLaren - 24 - - - - - sarah - sarah - Sarah Sims - 137 - - - - - ajc - ajc@sanger.ac.uk - Alison J Coffey - 129 - - - - - 2009-04-16 17:58:19 +0100 - 2009-11-05 16:00:26 +0000 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - - - - Policy - - - - Study description - - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - - - - ENA Study Accession Number - - - - Title - - - - Abstract - - - - ENA Project ID - - - - Study Type - Not specified - - - Faculty Sponsor - None - - - What sort of study is this? - not specified - - - Reference Genome - - - - diff --git a/t/data/st_api_lims_new/st/studies/297.xml b/t/data/st_api_lims_new/st/studies/297.xml deleted file mode 100644 index 0bf214d4..00000000 --- a/t/data/st_api_lims_new/st/studies/297.xml +++ /dev/null @@ -1,189 +0,0 @@ - - - 297 - Discovery of sequence diversity in Shigella sp. - true - 206 - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - tc7 - tc7@sanger.ac.uk - Thomas Connor - 475 - - - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - jm15 - jm15@sanger.ac.uk - Jacqueline McQuillan - 67 - - - nds - nds@sanger.ac.uk - Nishadi De Silva - 383 - - - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - - - 2009-04-27 11:46:48 +0100 - 2010-09-09 14:27:54 +0100 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - standard - - - Policy - - - - Study description - For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/shigella-sonnei.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - open - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - No - - - ENA Study Accession Number - ERP000182 - - - Title - Discovery of sequence diversity in Shigella sp. - - - Abstract - For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/shigella-sonnei.html - - - ENA Project ID - - - - Study Type - Whole Genome Sequencing - - - Faculty Sponsor - Julian Parkhill - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - diff --git a/t/data/st_api_lims_new/st/studies/429.xml b/t/data/st_api_lims_new/st/studies/429.xml deleted file mode 100644 index 7cd17b72..00000000 --- a/t/data/st_api_lims_new/st/studies/429.xml +++ /dev/null @@ -1,157 +0,0 @@ - - - 429 - 3C and HiC of Plasmodium falciparum IT - true - 29 - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - 2010-01-11 15:14:58 +0000 - 2011-05-03 16:23:09 +0100 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - false - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - standard - - - Policy - - - - Study description - Illumina sequencing of chromatin conformation capture and its derivatives is being carried out to study nuclear architecture in antigenically selected lines of Plasmodium falciparum. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - open - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - No - - - ENA Study Accession Number - - - - Title - Genome-Wide Subnuclear Architecture in Antigenically Selected Lines of P.falciparum - - - Abstract - We have used chromatin conformation capture and its derivatives to study the nuclear architecture in lines of P.falciparum that express distinct variant antigens. Chemical crosslinking of cells followed by proximity based ligation and the subsequent enrichment of ligated junctions allows us to estimate contact probabilities for all genomic loci at a resolution of 10kB - 100kB. We evaluate these contact probabilities in the context of polymer folding models to deduce the scaling principles and folding architecture of interphase P. falciparum chromosomes. We consider evidence for spatial segregation of subtelomeric chromosomal territories involved in var gene expression as well as the anchoring of heterochromatic regions to the nuclear periphery. - - - ENA Project ID - 0 - - - Study Type - Epigenetics - - - Faculty Sponsor - Matt Berriman - - - What sort of study is this? - transcriptomics - - - Reference Genome - - - - diff --git a/t/data/st_api_lims_new/st/studies/700.xml b/t/data/st_api_lims_new/st/studies/700.xml deleted file mode 100644 index d56ad2a9..00000000 --- a/t/data/st_api_lims_new/st/studies/700.xml +++ /dev/null @@ -1,171 +0,0 @@ - - - 700 - Kapa HiFi test - true - 7 - - - mq1 - mq1@sanger.ac.uk - Michael Quail - 7 - - - ems - ems@sanger.ac.uk - Elizabeth Sheridan - 72 - - - - - mq1 - mq1@sanger.ac.uk - Michael Quail - 7 - - - - - 2010-10-07 16:11:00 +0100 - 2010-10-21 11:03:52 +0100 - - - SNP study ID - - - - What is the reason for preventing data release? - data validity - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - Data generated is for testing of new methodology. These genomes have already been sequenced and so release would not serve any purpose - - - How is the data release to be timed? - never - - - Policy - - - - Study description - − I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. -− If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage. -− In theory kapa hifi has higher fidelity than phusion. - - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - Yes - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - Yes - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - managed - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - No - - - ENA Study Accession Number - - - - Title - hifi test - - - Abstract - Purpose of experiment - -− To evaluate kapa hifi qPCR kit -− To evaluate kapa hifi and "robust" enzymes as alternatives to phusion. How do libraries prepared with these enzymes compare in terms of fidelity and coverage? -− To generate data on test genomes that can be used in Pacbio data analysis - - - - ENA Project ID - 0 - - - Study Type - Whole Genome Sequencing - - - Faculty Sponsor - Harold Swerdlow - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - diff --git a/t/data/st_api_lims_new/st/studies/701.xml b/t/data/st_api_lims_new/st/studies/701.xml deleted file mode 100644 index a19371c2..00000000 --- a/t/data/st_api_lims_new/st/studies/701.xml +++ /dev/null @@ -1,224 +0,0 @@ - - - 701 - Kuusamo - true - 82 - - - ak6 - ak6@sanger.ac.uk - Anja Kolb-Kokocinski - 224 - - - elg - elg@sanger.ac.uk - Emma Gray - 236 - - - kp5 - kp5@sanger.ac.uk - Kimmo Palin - 158 - - - eh4 - eh4@sanger.ac.uk - Eija Hamalainen - 337 - - - tk2 - thomas.keane@sanger.ac.uk - Thomas Keane - 43 - - - - - jws - jws@sanger.ac.uk - James Stalker - 82 - - - sarah - sarah - Sarah Sims - 137 - - - ak6 - ak6@sanger.ac.uk - Anja Kolb-Kokocinski - 224 - - - - - rd - rd@sanger.ac.uk - Richard Durbin - 8 - - - - - 2010-10-08 12:27:10 +0100 - 2012-11-26 14:15:35 +0000 - - - Study description - The aim of this study is to characterize as completely as possible the genetic variation and structure of Kuusamo and surrounding regions. We will perform low coverage, whole genome sequencing in a relatively limited number (approximately 200) of individuals from the FINRISK study both of whose parents are born in Kuusamo, Posio or Taivalkoski. Sequencing will be performed at the Wellcome Trust Sanger Institute (WTSI). We have previously shown using simulations and genome wide SNP data that the genetic characteristics agree with known genealogical data, and that approximately 200 individuals suffice to capture the majority of the genetic variation in this population. - -We have also developed methods for long-range haplotyping and long-range imputation, which are more accurate than traditional methods. This will allow us to identify a majority of the founder haplotypes in this population. The information from the haplotypes identified in this study can be used in other studies to impute from genome-wide SNP data the full genome sequence of samples ascertained for specific phenotypes. - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - 0 - - - Abstract - In this study, we aim to fully characterize a very high proportion of the genetic variation in a population. Information obtained from this study can be used by imputation in other studies aiming to identify genetic risk factors for disorders in the same population. It will also serve as a proof-of-principle study and allow method development for other similar projects in the future involving sequencing of other population isolates. - - - Title - Genetic variation in Kuusamo - - - ENA Study Accession Number - EGAS00001000020 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - KUU - - - What is the data release strategy for this study? - managed - - - Will you be using WTSI's standard access agreement? - Yes - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - false - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - http://www.sanger.ac.uk/datasharing/ - - - Policy title - - - - EGA DAC Accession Number - EGAC00001000039 - - - EGA Policy Accession Number - EGAP00001000041 - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Population Genomics - - - What sort of study is this? - genomic sequencing - - - Reference Genome - Homo_sapiens (1000Genomes_hs37d5) - - - Faculty Sponsor - Richard Durbin - -Data access groupkuusamo - - diff --git a/t/data/tag_from_sample_description/st/batches/19158.xml b/t/data/tag_from_sample_description/st/batches/19158.xml deleted file mode 100644 index 6724bf6d..00000000 --- a/t/data/tag_from_sample_description/st/batches/19158.xml +++ /dev/null @@ -1,402 +0,0 @@ - - - 19158 - released - 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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2236 - diff --git a/t/data/tag_from_sample_description/st/samples/1448209.xml b/t/data/tag_from_sample_description/st/samples/1448209.xml deleted file mode 100644 index cfce1728..00000000 --- a/t/data/tag_from_sample_description/st/samples/1448209.xml +++ /dev/null @@ -1,244 +0,0 @@ - - - 1448209 - PD9925c_rs - 2236 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - Genomic - - - Public Name - PD9925c - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001072684 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2236 - diff --git a/t/data/tag_from_sample_description/st/samples/1448210.xml b/t/data/tag_from_sample_description/st/samples/1448210.xml deleted file mode 100644 index ad840cc7..00000000 --- a/t/data/tag_from_sample_description/st/samples/1448210.xml +++ /dev/null @@ -1,244 +0,0 @@ - - - 1448210 - PD9926c_rs - 2236 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - Genomic - - - Public Name - PD9926c - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001072685 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2236 - diff --git a/t/data/tag_from_sample_description/st/samples/1448211.xml b/t/data/tag_from_sample_description/st/samples/1448211.xml deleted file mode 100644 index 1e934489..00000000 --- a/t/data/tag_from_sample_description/st/samples/1448211.xml +++ /dev/null @@ -1,244 +0,0 @@ - - - 1448211 - PD9927c_rs - 2236 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - Genomic - - - Public Name - PD9927c - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001072686 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2236 - diff --git a/t/data/tag_from_sample_description/st/samples/1448212.xml b/t/data/tag_from_sample_description/st/samples/1448212.xml deleted file mode 100644 index f40420a0..00000000 --- a/t/data/tag_from_sample_description/st/samples/1448212.xml +++ /dev/null @@ -1,244 +0,0 @@ - - - 1448212 - PD9928c_rs - 2236 - false - - - Organism - Human - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - DNA source - Genomic - - - Public Name - PD9928c - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001072687 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 2236 - diff --git a/t/data/tag_from_sample_description/st/samples/1503349.xml b/t/data/tag_from_sample_description/st/samples/1503349.xml deleted file mode 100644 index 5c1fafcf..00000000 --- a/t/data/tag_from_sample_description/st/samples/1503349.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1503349 - dag1_mut1 - 82 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - DNA source - Genomic - - - Public Name - Zebrafish dag1 mut1 - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS183150 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from dag1 knockout incross 1. A 6 base indexing sequence (TAGACA) is bases 5 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching - day 2 ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - - 82 - - diff --git a/t/data/tag_from_sample_description/st/samples/1503350.xml b/t/data/tag_from_sample_description/st/samples/1503350.xml deleted file mode 100644 index f38d4301..00000000 --- a/t/data/tag_from_sample_description/st/samples/1503350.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1503350 - dag1_wt1 - 82 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - DNA source - Genomic - - - Public Name - Zebrafish dag1 wt1 - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS183151 - - - Sample Description - 3' end enriched mRNA from morphologically normal sibling embryos from dag1 knockout incross 1. A 6 base indexing sequence (CTACCA) is bases 5 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching - day 2 ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - - 82 - - diff --git a/t/data/tag_from_sample_description/st/samples/1503351.xml b/t/data/tag_from_sample_description/st/samples/1503351.xml deleted file mode 100644 index 57a50012..00000000 --- a/t/data/tag_from_sample_description/st/samples/1503351.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1503351 - dag1_mut2 - 82 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - DNA source - Genomic - - - Public Name - Zebrafish dag1 mut2 - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS183152 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from dag1 knockout incross 2. A 6 base indexing sequence (TATCTA) is bases 5 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching - day 2 ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - - 82 - - diff --git a/t/data/tag_from_sample_description/st/samples/1503352.xml b/t/data/tag_from_sample_description/st/samples/1503352.xml deleted file mode 100644 index 57a50012..00000000 --- a/t/data/tag_from_sample_description/st/samples/1503352.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1503351 - dag1_mut2 - 82 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - DNA source - Genomic - - - Public Name - Zebrafish dag1 mut2 - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS183152 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from dag1 knockout incross 2. A 6 base indexing sequence (TATCTA) is bases 5 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching - day 2 ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - - 82 - - diff --git a/t/data/tag_from_sample_description/st/samples/1503353.xml b/t/data/tag_from_sample_description/st/samples/1503353.xml deleted file mode 100644 index b37543cf..00000000 --- a/t/data/tag_from_sample_description/st/samples/1503353.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1503353 - dag1_mut3 - 82 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - DNA source - Genomic - - - Public Name - Zebrafish dag1 mut3 - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS183154 - - - Sample Description - 3' end enriched mRNA from morphologically abnormal embryos from dag1 knockout incross 3. A 6 base indexing sequence (GTAGAC) is bases 5 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching - day 2 ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - - 82 - diff --git a/t/data/tag_from_sample_description/st/samples/1503354.xml b/t/data/tag_from_sample_description/st/samples/1503354.xml deleted file mode 100644 index da0019bd..00000000 --- a/t/data/tag_from_sample_description/st/samples/1503354.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 1503354 - dag1_wt3 - 82 - false - - - Organism - zebrafish - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Unknown - - - DNA source - Genomic - - - Public Name - Zebrafish dag1 wt3 - - - Common Name - Danio rerio - - - Strain - mixed - - - TAXON ID - 7955 - - - ENA Sample Accession Number - ERS183155 - - - Sample Description - 3' end enriched mRNA from morphologically normal sibling embryos from dag1 knockout incross 3. A 6 base indexing sequence (TTAATC) is bases 5 to 10 of read 1 followed by polyT. More information describing the mutant phenotype can be found at the Wellcome Trust Sanger Institute Zebrafish Mutation Project website http://www.sanger.ac.uk/cgi-bin/Projects/D_rerio/zmp/search.pl?q=zmp_phD - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - N/A - - - Age - N/A - - - Developmental Stage - Hatching - day 2 ZFS:0000033 - - - Cell Type - N/A - - - Disease State - N/A - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - - - - Organism Part - Whole Embryo - - - Time Point - N/A - - - Treatment - N/A - - - Subject - - - - Disease - N/A - - - Reference Genome - Danio_rerio (zv9) - - - - - - - - - - - 82 - - diff --git a/t/data/test40_lims_edited/st/batches/14706.xml b/t/data/test40_lims_edited/st/batches/14706.xml deleted file mode 100644 index 505563bc..00000000 --- a/t/data/test40_lims_edited/st/batches/14706.xml +++ /dev/null @@ -1,321 +0,0 @@ - - - 14706 - released - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - - - - - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - - - - 1 - TAGCTTGT - 5 - - - - - - 2 - CGATGTTT - 5 - - - - - - 3 - GCCAATGT - 5 - - - - - - 4 - ACAGTGGT - 5 - - - - - - 5 - ATCACGTT - 5 - - - - - - - diff --git a/t/data/test40_lims_edited/st/batches/4775.xml b/t/data/test40_lims_edited/st/batches/4775.xml deleted file mode 100644 index 7c928e9e..00000000 --- a/t/data/test40_lims_edited/st/batches/4775.xml +++ /dev/null @@ -1,101 +0,0 @@ - - - 4775 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - - - - - 1 - ATCACGTTAT - 7 - - - - - 2 - CGATGTTTAT - 7 - - - - - - 3 - TTAGGCATAT - 7 - - - - - - diff --git a/t/data/test40_lims_edited/st/samples/1093818.xml b/t/data/test40_lims_edited/st/samples/1093818.xml deleted file mode 100644 index 89b3cc38..00000000 --- a/t/data/test40_lims_edited/st/samples/1093818.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1093818 - SS109305 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SS109305 - - - Common Name - Shigella sonnei - - - Strain - 109305 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS024591 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/test40_lims_edited/st/samples/1093819.xml b/t/data/test40_lims_edited/st/samples/1093819.xml deleted file mode 100644 index c357a72c..00000000 --- a/t/data/test40_lims_edited/st/samples/1093819.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1093819 - SS109114 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SS109114 - - - Common Name - Shigella sonnei - - - Strain - 109114 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS024592 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/test40_lims_edited/st/samples/1093820.xml b/t/data/test40_lims_edited/st/samples/1093820.xml deleted file mode 100644 index c855037c..00000000 --- a/t/data/test40_lims_edited/st/samples/1093820.xml +++ /dev/null @@ -1,210 +0,0 @@ - - - 1093820 - SS117886 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - SS117886 - - - Common Name - Shigella sonnei - - - Strain - 117886 - - - TAXON ID - 624 - - - ENA Sample Accession Number - ERS024593 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - 297 - diff --git a/t/data/test40_lims_edited/st/samples/1296986.xml b/t/data/test40_lims_edited/st/samples/1296986.xml deleted file mode 100644 index d6f99f2f..00000000 --- a/t/data/test40_lims_edited/st/samples/1296986.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - 1296986 - 5_SB-induced_tumour_1 - 2012 - false - - - Organism - mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 5' SB-induced tumour 1 - - - Common Name - Mus Musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS069770 - - - Sample Description - transposon-induced tumour - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - cancer - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - N/A - - - Disease State - diseased - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - cancer - - - Reference Genome - Mus_musculus (std_unmasked_NCBIm37) - - - - - - 2012 - diff --git a/t/data/test40_lims_edited/st/samples/1296987.xml b/t/data/test40_lims_edited/st/samples/1296987.xml deleted file mode 100644 index 2ea00caa..00000000 --- a/t/data/test40_lims_edited/st/samples/1296987.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - 1296987 - 5_SB-induced_tumour_2 - 2012 - false - - - Organism - mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 5' SB-induced tumour 2 - - - Common Name - Mus Musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS069771 - - - Sample Description - transposon-induced tumour - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - cancer - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - N/A - - - Disease State - diseased - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - cancer - - - Reference Genome - Mus_musculus (std_unmasked_NCBIm37) - - - - - - 2012 - diff --git a/t/data/test40_lims_edited/st/samples/1296988.xml b/t/data/test40_lims_edited/st/samples/1296988.xml deleted file mode 100644 index 9efb62b4..00000000 --- a/t/data/test40_lims_edited/st/samples/1296988.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - 1296988 - 5_SB-induced_tumour_3 - 2012 - false - - - Organism - mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 5' SB-induced tumour 3 - - - Common Name - Mus Musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS069772 - - - Sample Description - transposon-induced tumour - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - cancer - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - N/A - - - Disease State - diseased - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - cancer - - - Reference Genome - Mus_musculus (std_unmasked_NCBIm37) - - - - - - 2012 - diff --git a/t/data/test40_lims_edited/st/samples/1296989.xml b/t/data/test40_lims_edited/st/samples/1296989.xml deleted file mode 100644 index bd3e2da6..00000000 --- a/t/data/test40_lims_edited/st/samples/1296989.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - 1296989 - 5_SB-induced_tumour_4 - 2012 - false - - - Organism - mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 5' SB-induced tumour 4 - - - Common Name - Mus Musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS069773 - - - Sample Description - transposon-induced tumour - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - cancer - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - N/A - - - Disease State - diseased - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - cancer - - - Reference Genome - Mus_musculus (std_unmasked_NCBIm37) - - - - - - 2012 - diff --git a/t/data/test40_lims_edited/st/samples/1296990.xml b/t/data/test40_lims_edited/st/samples/1296990.xml deleted file mode 100644 index 11f80067..00000000 --- a/t/data/test40_lims_edited/st/samples/1296990.xml +++ /dev/null @@ -1,205 +0,0 @@ - - - 1296990 - 5_SB-induced_tumour_5 - 2012 - false - - - Organism - mouse - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - Not Applicable - - - DNA source - Genomic - - - Public Name - 5' SB-induced tumour 5 - - - Common Name - Mus Musculus - - - Strain - - - - TAXON ID - 10090 - - - ENA Sample Accession Number - ERS069774 - - - Sample Description - transposon-induced tumour - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - N/A - - - Phenotype - cancer - - - Age - N/A - - - Developmental Stage - N/A - - - Cell Type - N/A - - - Disease State - diseased - - - Compound - N/A - - - Dose - N/A - - - Immunoprecipitate - N/A - - - Growth Condition - N/A - - - RNAi - N/A - - - Organism Part - N/A - - - Time Point - N/A - - - Treatment - N/A - - - Subject - N/A - - - Disease - cancer - - - Reference Genome - Mus_musculus (std_unmasked_NCBIm37) - - - - - - 2012 - diff --git a/t/data/test45/st/batches/13994.xml b/t/data/test45/st/batches/13994.xml deleted file mode 100644 index 31a7381c..00000000 --- a/t/data/test45/st/batches/13994.xml +++ /dev/null @@ -1,107 +0,0 @@ - - - 13994 - released - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - - diff --git a/t/data/test45/st/batches/15728.xml b/t/data/test45/st/batches/15728.xml deleted file mode 100644 index 3e742129..00000000 --- a/t/data/test45/st/batches/15728.xml +++ /dev/null @@ -1,815 +0,0 @@ - - - 15728 - released - - - - - - 1 - ATCACG - 3 - - - DDD custom library - - - - - - 2 - CGATGT - 3 - - - DDD custom library - - - - - - 3 - TTAGGC - 3 - - - DDD custom library - - - - - - 4 - TGACCA - 3 - - - DDD custom library - - - - - - 5 - ACAGTG - 3 - - - DDD custom library - - - - - - 6 - GCCAAT - 3 - - - DDD custom library - - - - - - 7 - CAGATC - 3 - - - DDD custom library - - - - - - 8 - ACTTGA - 3 - - - DDD custom library - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - DDD custom library - - - - - - 2 - CGATGT - 3 - - - DDD custom library - - - - - - 3 - TTAGGC - 3 - - - DDD custom library - - - - - - 4 - TGACCA - 3 - - - DDD custom library - - - - - - 5 - ACAGTG - 3 - - - DDD custom library - - - - - - 6 - GCCAAT - 3 - - - DDD custom library - - - - - - 7 - CAGATC - 3 - - - DDD custom library - - - - - - 8 - ACTTGA - 3 - - - DDD custom library - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - DDD custom library - - - - - - 2 - CGATGT - 3 - - - DDD custom library - - - - - - 3 - TTAGGC - 3 - - - DDD custom library - - - - - - 4 - TGACCA - 3 - - - DDD custom library - - - - - - 5 - ACAGTG - 3 - - - DDD custom library - - - - - - 6 - GCCAAT - 3 - - - DDD custom library - - - - - - 7 - CAGATC - 3 - - - DDD custom library - - - - - - 8 - ACTTGA - 3 - - - DDD custom library - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - DDD custom library - - - - - - 2 - CGATGT - 3 - - - DDD custom library - - - - - - 3 - TTAGGC - 3 - - - DDD custom library - - - - - - 4 - TGACCA - 3 - - - DDD custom library - - - - - - 5 - ACAGTG - 3 - - - DDD custom library - - - - - - 6 - GCCAAT - 3 - - - DDD custom library - - - - - - 7 - CAGATC - 3 - - - DDD custom library - - - - - - 8 - ACTTGA - 3 - - - DDD custom library - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - DDD custom library - - - - - - 2 - CGATGT - 3 - - - DDD custom library - - - - - - 3 - TTAGGC - 3 - - - DDD custom library - - - - - - 4 - TGACCA - 3 - - - DDD custom library - - - - - - 5 - ACAGTG - 3 - - - DDD custom library - - - - - - 6 - GCCAAT - 3 - - - DDD custom library - - - - - - 7 - CAGATC - 3 - - - DDD custom library - - - - - - 8 - ACTTGA - 3 - - - DDD custom library - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - DDD custom library - - - - - - 2 - CGATGT - 3 - - - DDD custom library - 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DDD custom library - - - - - - 5 - ACAGTG - 3 - - - DDD custom library - - - - - - 6 - GCCAAT - 3 - - - DDD custom library - - - - - - 7 - CAGATC - 3 - - - DDD custom library - - - - - - 8 - ACTTGA - 3 - - - DDD custom library - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - \ No newline at end of file diff --git a/t/data/test45/st/batches/16249.xml b/t/data/test45/st/batches/16249.xml deleted file mode 100644 index 41e34c1a..00000000 --- a/t/data/test45/st/batches/16249.xml +++ /dev/null @@ -1,771 +0,0 @@ - - - 16249 - released - - - - - - 1 - ATCACG - 3 - - - Human all exon 50MB - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - 3 - TTAGGC - 3 - - - Human all exon 50MB - - - - - - 4 - TGACCA - 3 - - - Human all exon 50MB - - - - - - 5 - ACAGTG - 3 - - - Human all exon 50MB - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - 7 - CAGATC - 3 - - - Human all exon 50MB - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - 168 - ACAACGCAAT - 6 - - - 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TGACCA - 3 - - - Human all exon 50MB - - - - - - 5 - ACAGTG - 3 - - - Human all exon 50MB - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - 7 - CAGATC - 3 - - - Human all exon 50MB - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - Human all exon 50MB - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - 3 - TTAGGC - 3 - - - Human all exon 50MB - - - - - - 4 - TGACCA - 3 - - - Human all exon 50MB - - - - - - 5 - ACAGTG - 3 - - - Human all exon 50MB - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - 7 - CAGATC - 3 - - - Human all exon 50MB - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - Human all exon 50MB - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - 3 - TTAGGC - 3 - - - Human all exon 50MB - - - - - - 4 - TGACCA - 3 - - - Human all exon 50MB - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - 7 - CAGATC - 3 - - - Human all exon 50MB - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 1 - ATCACG - 3 - - - Human all exon 50MB - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - 3 - TTAGGC - 3 - - - Human all exon 50MB - - - - - - 4 - TGACCA - 3 - - - Human all exon 50MB - - - - - - 5 - ACAGTG - 3 - - - Human all exon 50MB - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - 7 - CAGATC - 3 - - - Human all exon 50MB - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - - - - 2 - CGATGT - 3 - - - Human all exon 50MB - - - - - - 3 - TTAGGC - 3 - - - Human all exon 50MB - - - - - - 4 - TGACCA - 3 - - - Human all exon 50MB - - - - - - 5 - ACAGTG - 3 - - - Human all exon 50MB - - - - - - 6 - GCCAAT - 3 - - - Human all exon 50MB - - - - - - 7 - CAGATC - 3 - - - Human all exon 50MB - - - - - - 8 - ACTTGA - 3 - - - Human all exon 50MB - - - - - - - - 168 - ACAACGCAAT - 6 - - - - - - diff --git a/t/data/test45/st/batches/4775.xml b/t/data/test45/st/batches/4775.xml deleted file mode 100644 index 0712a6df..00000000 --- a/t/data/test45/st/batches/4775.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - 4775 - released - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/test45/st/batches/4861.xml b/t/data/test45/st/batches/4861.xml deleted file mode 100644 index 8fdd3968..00000000 --- a/t/data/test45/st/batches/4861.xml +++ /dev/null @@ -1,617 +0,0 @@ - - - 4861 - released - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - - - - - 1 - - 1 - - - - - - 2 - - 1 - - - - - - 3 - - 1 - - - - - - 4 - - 1 - - - - - - 5 - - 1 - - - - - - 6 - - 1 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - 12 - CTTGTA - 3 - - - - - - - - - - 1 - ATCACG - 3 - - - - - - 2 - CGATGT - 3 - - - - - - 3 - TTAGGC - 3 - - - - - - 4 - TGACCA - 3 - - - - - - 5 - ACAGTG - 3 - - - - - - 6 - GCCAAT - 3 - - - - - - 7 - CAGATC - 3 - - - - - - 8 - ACTTGA - 3 - - - - - - 9 - GATCAG - 3 - - - - - - 10 - TAGCTT - 3 - - - - - - 11 - GGCTAC - 3 - - - - - - 12 - CTTGTA - 3 - - - - - - - diff --git a/t/data/test45/st/batches/5647.xml b/t/data/test45/st/batches/5647.xml deleted file mode 100644 index 0b91a464..00000000 --- a/t/data/test45/st/batches/5647.xml +++ /dev/null @@ -1,1020 +0,0 @@ - - - 5647 - released - - - - - - 43 - TCATTGAG - 6 - - - - - - 44 - TGGCTCAG - 6 - - - - - - 45 - TATGCCAG - 6 - - - - - - 46 - TCAGATTC - 6 - - - - - - 47 - TACTAGTC - 6 - - - - - - 48 - TTCAGCTC - 6 - - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - 16 - TCCGTCTT - 6 - - - - - - 17 - TGTACCTT - 6 - - - - - - 18 - TTCTGTGT - 6 - - - - - - 19 - TCTGCTGT - 6 - - - - - - 20 - TTGGAGGT - 6 - - - - - - 21 - TCGAGCGT - 6 - - - - - - 22 - TGATACGT - 6 - - - - - - 23 - TGCATAGT - 6 - - - - - - 24 - TTGACTCT - 6 - - - - - - 25 - TGCGATCT - 6 - - - - - - 27 - TAGTGACT - 6 - - - - - - 28 - TACAGGAT - 6 - - - - - - 29 - TCCTCAAT - 6 - - - - - - 30 - TGTGGTTG - 6 - - - - - - 31 - TAGTCTTG - 6 - - - - - - 33 - TCGAAGTG - 6 - - - - - - 34 - TAACGCTG - 6 - - - - - - 35 - TTGGTATG - 6 - - - - - - 36 - TGAACTGG - 6 - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - 41 - TCCAGTCG - 6 - - - - - - 42 - TGTATGCG - 6 - - - - - - - - - - - - - - - - 43 - TCATTGAG - 6 - - - - - - 44 - TGGCTCAG - 6 - - - - - - 45 - TATGCCAG - 6 - - - - - - 46 - TCAGATTC - 6 - - - - - - 47 - TACTAGTC - 6 - - - - - - 48 - TTCAGCTC - 6 - - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - - - - - 1 - ATCACGTT - 6 - - - - - - 2 - CGATGTTT - 6 - - - - - - 3 - TTAGGCAT - 6 - - - - - - 4 - TGACCACT - 6 - - - - - - 5 - ACAGTGGT - 6 - - - - - - 6 - GCCAATGT - 6 - - - - - - 7 - CAGATCTG - 6 - - - - - - 8 - ACTTGATG - 6 - - - - - - 9 - GATCAGCG - 6 - - - - - - 10 - TAGCTTGT - 6 - - - - - - 11 - GGCTACAG - 6 - - - - - - 12 - CTTGTACT - 6 - - - - - - 13 - TGGTTGTT - 6 - - - - - - 14 - TCTCGGTT - 6 - - - - - - 15 - TAAGCGTT - 6 - - - - - - 16 - TCCGTCTT - 6 - - - - - - 17 - TGTACCTT - 6 - - - - - - 18 - TTCTGTGT - 6 - - - - - - 19 - TCTGCTGT - 6 - - - - - - 20 - TTGGAGGT - 6 - - - - - - 21 - TCGAGCGT - 6 - - - - - - 22 - TGATACGT - 6 - - - - - - 23 - TGCATAGT - 6 - - - - - - 24 - TTGACTCT - 6 - - - - - - 25 - TGCGATCT - 6 - - - - - - 27 - TAGTGACT - 6 - - - - - - 28 - TACAGGAT - 6 - - - - - - 29 - TCCTCAAT - 6 - - - - - - 30 - TGTGGTTG - 6 - - - - - - 31 - TAGTCTTG - 6 - - - - - - 33 - TCGAAGTG - 6 - - - - - - 34 - TAACGCTG - 6 - - - - - - 35 - TTGGTATG - 6 - - - - - - 36 - TGAACTGG - 6 - - - - - - 37 - TACTTCGG - 6 - - - - - - 38 - TCTCACGG - 6 - - - - - - 39 - TCAGGAGG - 6 - - - - - - 40 - TAAGTTCG - 6 - - - - - - 41 - TCCAGTCG - 6 - - - - - - 42 - TGTATGCG - 6 - - - - - - - - - - - - - - diff --git a/t/data/test45/st/batches/9589.xml b/t/data/test45/st/batches/9589.xml deleted file mode 100644 index d7f70c3c..00000000 --- a/t/data/test45/st/batches/9589.xml +++ /dev/null @@ -1,151 +0,0 @@ - - - 9589 - released - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - - - - 1 - ATCACGTT - 15 - - - - - 2 - CGATGTTT - 15 - - - - - - diff --git a/t/data/test45/st/projects/333.xml b/t/data/test45/st/projects/333.xml deleted file mode 100644 index e728dd14..00000000 --- a/t/data/test45/st/projects/333.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - 333 - CLL whole genome - true - active - - - Project funding model - external - own machine - - - External funding source - - - - Sequencing budget cost centre - - - - Project cost code - S0277 - - - Genotyping committee Tracking ID - - - - Collaborators - - - - Funding comments - - - - diff --git a/t/data/test45/st/projects/645.xml b/t/data/test45/st/projects/645.xml deleted file mode 100644 index 653fcbbc..00000000 --- a/t/data/test45/st/projects/645.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - 645 - UK10K - true - active - - - Project cost code - S0782 - - - Funding comments - - - - Collaborators - - - - External funding source - - - - Sequencing budget cost centre - - - - Project funding model - Internal - - - Genotyping committee Tracking ID - - - - diff --git a/t/data/test45/st/projects/678.xml b/t/data/test45/st/projects/678.xml deleted file mode 100644 index c754ab73..00000000 --- a/t/data/test45/st/projects/678.xml +++ /dev/null @@ -1,37 +0,0 @@ - - - 678 - MQ R and D - true - active - - - Project cost code - S0696 - - - Funding comments - R and D - - - Collaborators - - - - External funding source - - - - Sequencing budget cost centre - - - - Project funding model - Internal - - - Genotyping committee Tracking ID - - - - diff --git a/t/data/test45/st/samples/1015856.xml b/t/data/test45/st/samples/1015856.xml deleted file mode 100644 index f4e97326..00000000 --- a/t/data/test45/st/samples/1015856.xml +++ /dev/null @@ -1,221 +0,0 @@ - - - 1015856 - UK10K_ASDFI5007720 - 1681 - - - Time Point - - - - Organism Part - - - - Genotype - - - - Sample type - - - - Sample extraction method - - - - Father - - - - Plate - - - - Common Name - Homo sapiens - - - Gender - Female - - - Developmental Stage - - - - Concentration determind by - PicoGreen - - - Purification method - - - - Mother - - - - Growth Condition - - - - Dose - - - - Sibling - - - - Public Name - - - - Phenotype - - - - Is re-submitted? - false - - - ENA Sample Accession Number - EGAN00001014725 - - - Replicate - - - - Sample Description - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - DNA source - Blood - - - Volume (µl) - 123 - - - Ethnicity - Finnish - - - Organism - - - - Compound - - - - Age - - - - Date of sample collection - - - - TAXON ID - 9606 - - - RNAi - - - - Sample Visibility - - - - Strain - - - - Cohort - ASD_FI - - - Subject - - - - Treatment - - - - Concentration - 180 - - - Date of sample extraction - - - - Country of origin - Finland - - - Disease - - - - Disease State - - - - Sample storage conditions - -20C - - - Sample purified - N - - - GC content - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - 1681 - diff --git a/t/data/test45/st/samples/1015957.xml b/t/data/test45/st/samples/1015957.xml deleted file mode 100644 index 377a02f5..00000000 --- a/t/data/test45/st/samples/1015957.xml +++ /dev/null @@ -1,222 +0,0 @@ - - - 1015957 - UK10K_ASDFI5007878 - 1681 - - - Time Point - - - - Organism Part - - - - Genotype - - - - Sample type - - - - Sample extraction method - - - - Father - - - - Plate - - - - Common Name - Homo sapiens - - - Gender - Male - - - Developmental Stage - - - - Concentration determind by - PicoGreen - - - Purification method - - - - Mother - - - - Growth Condition - - - - Dose - - - - Sibling - - - - Public Name - - - - Phenotype - - - - Is re-submitted? - false - - - ENA Sample Accession Number - EGAN00001014843 - - - Replicate - - - - Sample Description - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - DNA source - Blood - - - Volume (µl) - 115 - - - Ethnicity - Finnish - - - Organism - - - - Compound - - - - Age - - - - Date of sample collection - - - - TAXON ID - 9606 - - - RNAi - - - - Sample Visibility - - - - Strain - - - - Cohort - ASD_FI - - - Subject - - - - Treatment - - - - Concentration - 94 - - - Date of sample extraction - - - - Country of origin - Finland - - - Disease - - - - Disease State - - - - Sample storage conditions - -20C - - - Sample purified - N - - - GC content - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - 1681 - diff --git a/t/data/test45/st/samples/1092799.xml b/t/data/test45/st/samples/1092799.xml deleted file mode 100644 index 0415162e..00000000 --- a/t/data/test45/st/samples/1092799.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092799 - UK10K_UKSCZ5072920 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Female - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017478 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092801.xml b/t/data/test45/st/samples/1092801.xml deleted file mode 100644 index 814a9f9d..00000000 --- a/t/data/test45/st/samples/1092801.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092801 - UK10K_UKSCZ5072921 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Female - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017479 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092803.xml b/t/data/test45/st/samples/1092803.xml deleted file mode 100644 index 8d93e97e..00000000 --- a/t/data/test45/st/samples/1092803.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092803 - UK10K_UKSCZ5072922 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017480 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092805.xml b/t/data/test45/st/samples/1092805.xml deleted file mode 100644 index 502b5cc4..00000000 --- a/t/data/test45/st/samples/1092805.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092805 - UK10K_UKSCZ5072923 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017481 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092807.xml b/t/data/test45/st/samples/1092807.xml deleted file mode 100644 index 469da3d9..00000000 --- a/t/data/test45/st/samples/1092807.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092807 - UK10K_UKSCZ5072924 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017482 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092809.xml b/t/data/test45/st/samples/1092809.xml deleted file mode 100644 index ad36584e..00000000 --- a/t/data/test45/st/samples/1092809.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092809 - UK10K_UKSCZ5072925 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017483 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092811.xml b/t/data/test45/st/samples/1092811.xml deleted file mode 100644 index b595889c..00000000 --- a/t/data/test45/st/samples/1092811.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092811 - UK10K_UKSCZ5072926 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 55 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001017484 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2011 - - - Date of sample extraction - 2011 - - - Sample extraction method - 8 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1092813.xml b/t/data/test45/st/samples/1092813.xml deleted file mode 100644 index 76d24296..00000000 --- a/t/data/test45/st/samples/1092813.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1092813 - UK10K_UKSCZ5072927 - 1679 - false - 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Genomic - - - Public Name - Plasmodium Falciparum - - - Common Name - Plasmodium Falciparum - - - Strain - 3D7 - - - TAXON ID - 5820 - - - ENA Sample Accession Number - - - - Sample Description - genomic DNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - Plasmodium_falciparum (3D7) - - - - - - - - - 700 - diff --git a/t/data/test45/st/samples/1289843.xml b/t/data/test45/st/samples/1289843.xml deleted file mode 100644 index 05c73706..00000000 --- a/t/data/test45/st/samples/1289843.xml +++ /dev/null @@ -1,212 +0,0 @@ - - - 1289843 - human400shear - 700 - false - - - Organism - Homo sapiens - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - Neutral - - - Gender - - - - Donor Id - - - - DNA source - Genomic - - - Public Name - Homo sapiens - - - Common Name - Human - - - Strain - colo_829 - - - TAXON ID - 9606 - - - ENA Sample Accession Number - - - - Sample Description - genomic DNA - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - Homo_sapiens (GRCh37_53) - - - - - - - - - 700 - diff --git a/t/data/test45/st/samples/1299717.xml b/t/data/test45/st/samples/1299717.xml deleted file mode 100644 index 77a19a58..00000000 --- a/t/data/test45/st/samples/1299717.xml +++ /dev/null @@ -1,238 +0,0 @@ - - - 1299717 - DDD_MAIN5245030 - 1834 - false - - - Organism - - - - Cohort - DDD_cohort - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 100.0 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - DDD_MAIN5245030 - - - DNA source - Saliva - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - 100.0 - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Not applicable - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1834 - diff --git a/t/data/test45/st/samples/1299722.xml b/t/data/test45/st/samples/1299722.xml deleted file mode 100644 index d1994384..00000000 --- a/t/data/test45/st/samples/1299722.xml +++ /dev/null @@ -1,237 +0,0 @@ - - - 1299722 - DDD_MAIN5245035 - 1834 - false - - - Organism - - - - Cohort - DDD_cohort - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - 100.0 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Female - - - Donor Id - DDD_MAIN5245035 - - - DNA source - Saliva - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - 100.0 - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - Not applicable - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1834 - diff --git a/t/data/test45/st/samples/1299723.xml b/t/data/test45/st/samples/1299723.xml deleted file mode 100644 index cc3199c1..00000000 --- a/t/data/test45/st/samples/1299723.xml +++ /dev/null @@ -1,232 +0,0 @@ - - - 1299723 - DDD_MAIN5245036 - 1834 - true - - - Growth Condition - - - - Compound - - - - Sample storage conditions - - - - Sample extraction method - - - - Subject - - - - Organism Part - - - - Father - - - - Country of origin - - - - Concentration - 100.0 - - - DNA source - Saliva - - - Dose - - - - Disease State - - - - Concentration determind by - - - - Purification method - - - - Sample Visibility - - - - Public Name - - - - Gender - Male - - - Volume (µl) - 100.0 - - - Developmental Stage - - - - Plate - - - - Ethnicity - - - - Organism - - - - Disease - - - - RNAi - - - - Phenotype - - - - Date of sample collection - - - - Is re-submitted? - - - - TAXON ID - 9606 - - - Sample type - - - - Sample purified - - - - ENA Sample Accession Number - - - - Strain - - - - GC content - - - - Genotype - - - - Date of sample extraction - - - - Sibling - - - - Mother - - - - Geographical region - - - - Immunoprecipitate - - - - Cell Type - - - - Replicate - - - - Cohort - DDD_cohort - - - Age - - - - Sample Description - - - - Common Name - Homo sapien - - - Treatment - - - - Time Point - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1834 - diff --git a/t/data/test45/st/samples/1318722.xml b/t/data/test45/st/samples/1318722.xml deleted file mode 100644 index e73c9401..00000000 --- a/t/data/test45/st/samples/1318722.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318722 - UK10K_UKSCZ5260646 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083713 - - - Sample Description - - - - Sample Visibility - Public - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 12 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318724.xml b/t/data/test45/st/samples/1318724.xml deleted file mode 100644 index 6a113472..00000000 --- a/t/data/test45/st/samples/1318724.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318724 - UK10K_UKSCZ5260647 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083715 - - - Sample Description - - - - Sample Visibility - Public - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 13 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318726.xml b/t/data/test45/st/samples/1318726.xml deleted file mode 100644 index 29e45170..00000000 --- a/t/data/test45/st/samples/1318726.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318726 - UK10K_UKSCZ5260648 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083717 - - - Sample Description - - - - Sample Visibility - Public - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 14 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318728.xml b/t/data/test45/st/samples/1318728.xml deleted file mode 100644 index e8b2a642..00000000 --- a/t/data/test45/st/samples/1318728.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318728 - UK10K_UKSCZ5260649 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083719 - - - Sample Description - - - - Sample Visibility - Public - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 15 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318730.xml b/t/data/test45/st/samples/1318730.xml deleted file mode 100644 index adba55d3..00000000 --- a/t/data/test45/st/samples/1318730.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1318730 - UK10K_UKSCZ5260650 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083721 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 16 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318732.xml b/t/data/test45/st/samples/1318732.xml deleted file mode 100644 index f396f168..00000000 --- a/t/data/test45/st/samples/1318732.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1318732 - UK10K_UKSCZ5260651 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083723 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 17 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318734.xml b/t/data/test45/st/samples/1318734.xml deleted file mode 100644 index e147558a..00000000 --- a/t/data/test45/st/samples/1318734.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1318734 - UK10K_UKSCZ5260652 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083725 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 18 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318737.xml b/t/data/test45/st/samples/1318737.xml deleted file mode 100644 index bae65065..00000000 --- a/t/data/test45/st/samples/1318737.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1318737 - UK10K_UKSCZ5260653 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Female - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083728 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 19 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318738.xml b/t/data/test45/st/samples/1318738.xml deleted file mode 100644 index bd43075c..00000000 --- a/t/data/test45/st/samples/1318738.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318738 - UK10K_UKSCZ5260654 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Female - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083729 - - - Sample Description - - - - Sample Visibility - Public - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 20 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318743.xml b/t/data/test45/st/samples/1318743.xml deleted file mode 100644 index 05b0d70a..00000000 --- a/t/data/test45/st/samples/1318743.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318743 - UK10K_UKSCZ5260656 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - 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- - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318758.xml b/t/data/test45/st/samples/1318758.xml deleted file mode 100644 index 87880f6e..00000000 --- a/t/data/test45/st/samples/1318758.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318758 - UK10K_UKSCZ5260664 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - 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diff --git a/t/data/test45/st/samples/1318759.xml b/t/data/test45/st/samples/1318759.xml deleted file mode 100644 index ddee39ef..00000000 --- a/t/data/test45/st/samples/1318759.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318759 - UK10K_UKSCZ5260665 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083750 - - - Sample Description - - - - Sample Visibility - Public - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 31 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318760.xml b/t/data/test45/st/samples/1318760.xml deleted file mode 100644 index 665cc759..00000000 --- a/t/data/test45/st/samples/1318760.xml +++ /dev/null @@ -1,235 +0,0 @@ - - - 1318760 - UK10K_UKSCZ5260666 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Female - 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- - 1318770 - UK10K_UKSCZ5260668 - 1679 - false - - - Organism - - - - Cohort - schiz - - - Country of origin - UK - - - Geographical region - - - - Ethnicity - Caucasian - - - Volume (µl) - 35 - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - Male - - - Donor Id - - - - DNA source - Blood - - - Public Name - - - - Common Name - Homo sapiens - - - Strain - - - - TAXON ID - 9606 - - - ENA Sample Accession Number - EGAN00001083761 - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 34 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - 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- - - Sibling - - - - Is re-submitted? - false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 35 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/1318773.xml b/t/data/test45/st/samples/1318773.xml deleted file mode 100644 index 53a1b104..00000000 --- a/t/data/test45/st/samples/1318773.xml +++ /dev/null @@ -1,233 +0,0 @@ - - - 1318773 - UK10K_UKSCZ5260670 - 1679 - false - 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false - - - Date of sample collection - 2010 - - - Date of sample extraction - 2010 - - - Sample extraction method - 37 - - - Sample purified - N - - - Purification method - - - - Concentration - 200 - - - Concentration determind by - PicoGreen - - - Sample type - - - - Sample storage conditions - -20C - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 1679 - diff --git a/t/data/test45/st/samples/5053.xml b/t/data/test45/st/samples/5053.xml deleted file mode 100644 index e45141a9..00000000 --- a/t/data/test45/st/samples/5053.xml +++ /dev/null @@ -1,208 +0,0 @@ - - - 5053 - DE1140 - 297 - false - - - Organism - Shigella sonnei - - - Cohort - - - - Country of origin - 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- - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 365 - diff --git a/t/data/test45/st/samples/8185.xml b/t/data/test45/st/samples/8185.xml deleted file mode 100644 index 76a5a2f8..00000000 --- a/t/data/test45/st/samples/8185.xml +++ /dev/null @@ -1,211 +0,0 @@ - - - 8185 - Control-5 - 365 - false - - - Organism - Plasmodium falciparum - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - high at - - - Gender - - - - DNA source - - - - Public Name - - - - Common Name - Plasmodium falciparum 3D7 - - - Strain - 3D7 - - - TAXON ID - 36329 - - - ENA Sample Accession Number - ERS005113 - - - Sample Description - - - - Sample Visibility - Hold - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - 365 - diff --git a/t/data/test45/st/samples/9836.xml b/t/data/test45/st/samples/9836.xml deleted file mode 100644 index aaedb241..00000000 --- a/t/data/test45/st/samples/9836.xml +++ /dev/null @@ -1,457 +0,0 @@ - - - 9836 - phiX CT1462-2 1 - false - - - Organism - - - - Cohort - - - - Country of origin - - - - Geographical region - - - - Ethnicity - - - - Volume (µl) - - - - Plate - - - - Mother - - - - Father - - - - Replicate - - - - GC content - - - - Gender - - - - Donor Id - - - - DNA source - - - - Public Name - - - - Common Name - - - - Strain - - - - TAXON ID - - - - ENA Sample Accession Number - - - - Sample Description - - - - Sample Visibility - - - - Sibling - - - - Is re-submitted? - - - - Date of sample collection - - - - Date of sample extraction - - - - Sample extraction method - - - - Sample purified - - - - Purification method - - - - Concentration - - - - Concentration determind by - - - - Sample type - - - - Sample storage conditions - - - - Genotype - - - - Phenotype - - - - Age - - - - Developmental Stage - - - - Cell Type - - - - Disease State - - - - Compound - - - - Dose - - - - Immunoprecipitate - - - - Growth Condition - - - - RNAi - - - - Organism Part - - - - Time Point - - - - Treatment - - - - Subject - - - - Disease - - - - Reference Genome - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/t/data/test45/st/studies/1679.xml b/t/data/test45/st/studies/1679.xml deleted file mode 100644 index acea9734..00000000 --- a/t/data/test45/st/studies/1679.xml +++ /dev/null @@ -1,213 +0,0 @@ - - - 1679 - UK10K_NEURO_UKSCZ - true - 82 - - - elg - elg@sanger.ac.uk - Emma Gray - 236 - - - cj5 - cj5@sanger.ac.uk - Chris Joyce - 305 - - - - - jws - jws@sanger.ac.uk - James Stalker - 82 - - - sm15 - sm15@sanger.ac.uk - Shane McCarthy - 618 - - - - - jws - jws@sanger.ac.uk - James Stalker - 82 - - - sm15 - sm15@sanger.ac.uk - Shane McCarthy - 618 - - - - - 2010-11-18 11:24:33 +0000 - 2013-04-05 12:19:51 +0100 - - - Study description - In the UK10K project we propose a series of complementary genetic approaches to find new low frequency/rare variants contributing to disease phenotypes. These will be based on obtaining the genome wide sequence of 4000 samples from the TwinsUK and ALSPAC cohorts (at 6x sequence coverage), and the exome sequence (protein coding regions and related conserved sequence) of 6000 samples selected for extreme phenotypes. Our studies will focus primarily on cardiovascular-related quantitative traits, obesity and related metabolic traits, neurodevelopmental disorders and a limited number of extreme clinical phenotypes that will provide proof-of-concept for future familial trait sequencing. We will analyse directly quantitative traits in the cohorts and the selected traits in the extreme samples, and also use imputation down to 0.1% allele frequency to extend the analyses to further sample sets with genome wide genotype data. In each case we will investigate indels and larger structural variants as well as SNPs, and use statistical methods that combine rare variants in a locus or pathway as well as single-variant approaches. - -The UK schizophrenia samples will be part of the neurodevelopmental disease group, and will undergo exome sequencing. - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - 0 - - - Abstract - The samples from patients with schizophrenia have been collected -systematically across community mental health teams and clinics in South -Wales. All samples are from UK Caucasian participants. The -UK10K_NEURO_UKSCZ sample set also includes samples from participant's -relatives (without schizophrenia/psychosis). - - - Title - UK10K exome sequence: UK schizophrenia samples - - - ENA Study Accession Number - EGAS00001000123 - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - Yes - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - UK10K_UKSCZ - - - What is the data release strategy for this study? - managed - - - Will you be using WTSI's standard access agreement? - No - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - EGAC00001000024 - - - EGA Policy Accession Number - EGAP00001000021 - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Exome Sequencing - - - What sort of study is this? - genomic sequencing - - - Reference Genome - Homo_sapiens (1000Genomes) - - - Faculty Sponsor - Richard Durbin - - - diff --git a/t/data/test45/st/studies/198.xml b/t/data/test45/st/studies/198.xml deleted file mode 100644 index e2ad4aad..00000000 --- a/t/data/test45/st/studies/198.xml +++ /dev/null @@ -1,181 +0,0 @@ - - - 198 - Illumina Controls - true - 83 - - - hps - hps@sanger.ac.uk - Harold Swerdlow - 83 - - - - - hps - hps@sanger.ac.uk - Harold Swerdlow - 83 - - - - - 2008-11-13 13:27:48 +0000 - 2013-08-12 14:14:01 +0100 - - - Study description - None - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - - - - Abstract - - - - Title - - - - ENA Study Accession Number - - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - No - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - open - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - standard - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - - - - Has this been approved? - - - - Comment regarding prevention of data release and approval - - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Resequencing - - - What sort of study is this? - genotyping or cytogenetics - - - Reference Genome - - - - Faculty Sponsor - None - - - diff --git a/t/data/test45/st/studies/297.xml b/t/data/test45/st/studies/297.xml deleted file mode 100644 index 34ccaa7b..00000000 --- a/t/data/test45/st/studies/297.xml +++ /dev/null @@ -1,193 +0,0 @@ - - - 297 - Discovery of sequence diversity in Shigella sp. - true - 206 - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - tc7 - tc7@sanger.ac.uk - Thomas Connor - 475 - - - - - deh - deh@sanger.ac.uk - David Harris - 138 - - - jm15 - jm15@sanger.ac.uk - Jacqueline McQuillan - 67 - - - nds - nds@sanger.ac.uk - Nishadi De Silva - 383 - - - - - tfelt - tfelt@sanger.ac.uk - Theresa Feltwell - 112 - - - - - 2009-04-27 11:46:48 +0100 - 2010-09-09 14:27:54 +0100 - - - Has this been approved? - - - - Delay for - - - - Study description - For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/shigella-sonnei.html This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - ENA Study Accession Number - ERP000182 - - - Title - Discovery of sequence diversity in Shigella sp. - - - SNP study ID - - - - Abstract - For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/shigella-sonnei.html - - - Study name abbreviation - - - - Do any of the samples in this study contain human DNA? - No - - - Study Visibility - Hold - - - Has the delay period been approved by the data sharing committee for this project? - - - - ArrayExpress Accession Number - - - - How is the data release to be timed? - standard - - - SNP parent study ID - - - - EGA DAC Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - What is the data release strategy for this study? - open - - - EGA Policy Accession Number - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Reason for delaying release - - - - Policy - - - - ENA Project ID - - - - Comment regarding prevention of data release and approval - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Comment regarding data release timing and approval - - - - Alignments in BAM - true - - - Will you be using WTSI's standard access agreement? - - - - Faculty Sponsor - Julian Parkhill - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Study Type - Whole Genome Sequencing - - - diff --git a/t/data/test45/st/studies/333.xml b/t/data/test45/st/studies/333.xml deleted file mode 100644 index 4954d12a..00000000 --- a/t/data/test45/st/studies/333.xml +++ /dev/null @@ -1,179 +0,0 @@ - - - 333 - CLL whole genome - true - 145 - - - las - las@sanger.ac.uk - Lucy Stebbings - 21 - - - pc8 - pc8@sanger.ac.uk - Peter Campbell - 51 - - - dg10 - dg10@sanger.ac.uk - Danushka Galappaththige - 300 - - - - - sm2 - sm2@sanger.ac.uk - Stuart McLaren - 145 - - - - - sm2 - sm2@sanger.ac.uk - Stuart McLaren - 145 - - - - - 2009-06-24 17:43:05 +0100 - 2010-03-23 16:34:10 +0000 - - - SNP study ID - - - - What is the reason for preventing data release? - - - - ArrayExpress Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - Alignments in BAM - true - - - Reason for delaying release - - - - Comment regarding prevention of data release and approval - - - - How is the data release to be timed? - standard - - - Policy - - - - Study description - Genomic libraries (500 bps) will be generated from total genomic DNA derived from a range of cancer samples and subjected paired end sequencing on the llumina GA. Paired reads will be mapped to build 37 of the human reference genome to facilitate the generation of genome wide copy number information, and the identification of novel rearranged cancer genes and gene fusions. - - - - EGA Policy Accession Number - - - - Will you be using WTSI's standard access agreement? - No - - - Study name abbreviation - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Study Visibility - Hold - - - Delay for - - - - SNP parent study ID - - - - Comment regarding data release timing and approval - - - - EGA DAC Accession Number - - - - Has this been approved? - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the data release strategy for this study? - managed - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Do any of the samples in this study contain human DNA? - Yes - - - ENA Study Accession Number - EGAS00001000014 - - - Title - CLL Cancer Whole Genome Sequencing - - - Abstract - The aim of this project is to identify the somatic mutations and hence the genes involved in the development of chronic lymphocytic leukemia critical through the sequencing of chronic lymphocytic leukemia cancer genomes and normal DNAs from the same individuals. Tumour DNA will be analysed and compared to matching constitutional (normal) DNA from the same patient to identify tumour-acquired (somatic) alterations. These alterations (mutations, copy number alterations, translocations and other genomic aberrations) will be identified in multiple tumours and then these sets will be compared against each other to determine which genes are mutated in common and which pathways have been targeted - - - - ENA Project ID - 0 - - - Study Type - Cancer Genomics - - - Faculty Sponsor - Peter Campbell - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - diff --git a/t/data/test45/st/studies/365.xml b/t/data/test45/st/studies/365.xml deleted file mode 100644 index 6f9d50d2..00000000 --- a/t/data/test45/st/studies/365.xml +++ /dev/null @@ -1,161 +0,0 @@ - - - 365 - Plasmodium falciparum 3D7 ChIP-Seq - false - 29 - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - mjs - mjs@sanger.ac.uk - Mandy Sanders - 29 - - - - - 2009-08-20 11:52:43 +0100 - 2010-03-23 16:54:36 +0000 - - - Has this been approved? - - - - Delay for - - - - Study description - Multiplex sequencing of ChIP derived fragments of Plasmodium falciparum 3D7. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/ - - - ENA Study Accession Number - - - - Title - - - - SNP study ID - - - - Abstract - - - - Study name abbreviation - - - - Do any of the samples in this study contain human DNA? - Yes - - - Study Visibility - Hold - - - Has the delay period been approved by the data sharing committee for this project? - - - - ArrayExpress Accession Number - - - - How is the data release to be timed? - standard - - - SNP parent study ID - - - - EGA DAC Accession Number - - - - Please explain the reason for delaying release (e.g., pre-existing collaborative agreement) - - - - What is the data release strategy for this study? - open - - - EGA Policy Accession Number - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - Yes - - - Reason for delaying release - - - - Policy - - - - ENA Project ID - - - - Comment regarding prevention of data release and approval - - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Number of gigabases per sample (minimum 0.15) - - - - What is the reason for preventing data release? - - - - Comment regarding data release timing and approval - - - - Alignments in BAM - true - - - Will you be using WTSI's standard access agreement? - - - - Faculty Sponsor - Matt Berriman - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Study Type - Epigenetics - - - diff --git a/t/data/test45/st/studies/700.xml b/t/data/test45/st/studies/700.xml deleted file mode 100644 index 95244282..00000000 --- a/t/data/test45/st/studies/700.xml +++ /dev/null @@ -1,195 +0,0 @@ - - - 700 - Kapa HiFi test - true - 7 - - - mq1 - mq1@sanger.ac.uk - Michael Quail - 7 - - - ems - ems@sanger.ac.uk - Elizabeth Sheridan - 72 - - - - - mq1 - mq1@sanger.ac.uk - Michael Quail - 7 - - - - - 2010-10-07 16:11:00 +0100 - 2012-11-26 14:15:35 +0000 - - - Study description - − I have agreed to alpha test the kapa hifi qPCR kit. This allows prep PCR to be followed in real time and stopped when sufficient product has accumulated so preventing overcycling and allowing user to interrogate prep PCR step. -− If we are to use this enzyme we need to know that it is at least as good as Phusion in terms of fidelity and coverage. -− In theory kapa hifi has higher fidelity than phusion. - - - - Does this study contain samples that are contaminated with human DNA which must be removed prior to analysis? - No - - - Does this study require the removal of X chromosome and autosome sequence? - No - - - Does this study require y chromosome data to be separated from x and autosomal data before archival? - false - - - ENA Project ID - 0 - - - Abstract - Purpose of experiment - -− To evaluate kapa hifi qPCR kit -− To evaluate kapa hifi and "robust" enzymes as alternatives to phusion. How do libraries prepared with these enzymes compare in terms of fidelity and coverage? -− To generate data on test genomes that can be used in Pacbio data analysis - - - - Title - hifi test - - - ENA Study Accession Number - - - - Study Visibility - Hold - - - Do any of the samples in this study contain human DNA? - No - - - Are all the samples to be used in this study commercially available, unlinked anonymised cell-lines? - No - - - Study name abbreviation - - - - What is the data release strategy for this study? - not applicable - - - Will you be using WTSI's standard access agreement? - - - - How is the data release to be timed? - never - - - Reason for delaying release - - - - Delay for - - - - Alignments in BAM - true - - - Please explain the reason for delaying release - - - - Comment regarding data release timing and approval - - - - Policy Url - - - - Policy title - - - - EGA DAC Accession Number - - - - EGA Policy Accession Number - - - - ArrayExpress Accession Number - - - - Has the delay period been approved by the data sharing committee for this project? - - - - What is the reason for preventing data release? - data validity - - - Has this been approved? - Yes - - - Comment regarding prevention of data release and approval - R+D Project - - - Data access group - - - - SNP study ID - - - - SNP parent study ID - - - - Number of gigabases per sample (minimum 0.15) - - - - HMDMC approval number - - - - Study Type - Whole Genome Sequencing - - - What sort of study is this? - genomic sequencing - - - Reference Genome - - - - Faculty Sponsor - Harold Swerdlow - - - diff --git a/t/useragent.pm b/t/useragent.pm deleted file mode 100644 index 8358f34c..00000000 --- a/t/useragent.pm +++ /dev/null @@ -1,99 +0,0 @@ -package t::useragent; -use strict; -use warnings; -use Test::More; -use English qw(-no_match_vars); -use Carp; - -sub new { - my ($class, $ref) = @_; - $ref ||= {}; - $ref->{'mock'} ||= {}; - - if(!exists $ref->{is_success}) { - carp qq(Did you mean to leave ua->{'is_success'} unset?); - } - $ref->{last_request} = []; - - return bless $ref, $class; -} - -sub mock { - my ($self, $mock) = @_; - if($mock) { - $self->{mock} = $mock; - } - return $self->{mock}; -} - -sub last_request { - my ($self, $last_request) = @_; - if($last_request) { - push @{$self->{last_request}}, $last_request; - } - return $self->{last_request}->[-1] || {}; -} - -sub requests { - my $self = shift; - return $self->{last_request}; -} - -sub get { - my ($self, $uri) = @_; - $self->{'uri'} = $uri; - return $self; -} - -sub post { - my ($self, $uri, %args) = @_; - $self->{uri} = $uri; - push @{$self->{last_request}}, \%args; - return $self; -} - -sub request { - my ($self, $req) = @_; - $self->{uri} = $req->uri(); - push @{$self->{last_request}}, $req; - return $self; -} - -sub requests_redirectable { - my $self = shift; - return []; -} - -sub content { - my $self = shift; - - my $test_data = $self->{mock}->{$self->{uri}}; - if (!$test_data) { - croak qq(No mock data configured for $self->{'uri'}); - } - - if ($test_data && $test_data =~ /^t\/|\/tmp\//sm) { - open my $fh, q(<), $test_data or croak qq(Error opening '$test_data': $ERRNO); - local $RS = undef; - my $content = <$fh>; - close $fh; - return $content; - } - return $test_data; -} - -sub decoded_content { - my $self = shift; - return $self->content(); -} - -sub response { my $self = shift; return $self; } -sub is_success { my $self = shift; return $self->{'is_success'}; } -sub status_line { return 'error in t::useragent'; } -sub headers { - my $self = shift; - return $self; -} -sub header { return q[]; } - -1; From 54a46ad50e4c5257a740a010c9c036fbc8ef0c83 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 23 Oct 2023 17:11:34 +0100 Subject: [PATCH 10/35] Updated DBIx classes from the prod database. Changes are due to the MySQL database server upgrade to v8.+ --- lib/npg_tracking/Schema/Result/Annotation.pm | 6 +++--- lib/npg_tracking/Schema/Result/Event.pm | 8 ++++---- lib/npg_tracking/Schema/Result/EventType.pm | 6 +++--- lib/npg_tracking/Schema/Result/Instrument.pm | 6 +++--- lib/npg_tracking/Schema/Result/InstrumentAnnotation.pm | 8 ++++---- .../Schema/Result/InstrumentDesignation.pm | 8 ++++---- lib/npg_tracking/Schema/Result/InstrumentFormat.pm | 6 +++--- lib/npg_tracking/Schema/Result/InstrumentMod.pm | 10 +++++----- lib/npg_tracking/Schema/Result/InstrumentStatus.pm | 10 +++++----- .../Schema/Result/InstrumentStatusAnnotation.pm | 8 ++++---- .../Schema/Result/InstrumentUtilisation.pm | 6 +++--- lib/npg_tracking/Schema/Result/Run.pm | 8 ++++---- lib/npg_tracking/Schema/Result/RunAnnotation.pm | 8 ++++---- lib/npg_tracking/Schema/Result/RunLane.pm | 6 +++--- lib/npg_tracking/Schema/Result/RunLaneAnnotation.pm | 8 ++++---- lib/npg_tracking/Schema/Result/RunLaneStatus.pm | 10 +++++----- lib/npg_tracking/Schema/Result/RunStatus.pm | 10 +++++----- lib/npg_tracking/Schema/Result/StCache.pm | 6 +++--- lib/npg_tracking/Schema/Result/TagFrequency.pm | 8 ++++---- lib/npg_tracking/Schema/Result/TagRun.pm | 10 +++++----- lib/npg_tracking/Schema/Result/TagRunLane.pm | 10 +++++----- lib/npg_tracking/Schema/Result/User2usergroup.pm | 8 ++++---- 22 files changed, 87 insertions(+), 87 deletions(-) diff --git a/lib/npg_tracking/Schema/Result/Annotation.pm b/lib/npg_tracking/Schema/Result/Annotation.pm index c3836457..5e8953de 100644 --- a/lib/npg_tracking/Schema/Result/Annotation.pm +++ b/lib/npg_tracking/Schema/Result/Annotation.pm @@ -193,12 +193,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:38 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:fw1PGLynbasn+IKgeZzzTw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:21CP732yEziG9roi+KTB8Q # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/Event.pm b/lib/npg_tracking/Schema/Result/Event.pm index 76e9f20c..8c20e311 100644 --- a/lib/npg_tracking/Schema/Result/Event.pm +++ b/lib/npg_tracking/Schema/Result/Event.pm @@ -165,7 +165,7 @@ __PACKAGE__->belongs_to( "event_type", "npg_tracking::Schema::Result::EventType", { id_event_type => "id_event_type" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -180,12 +180,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-28 12:00:59 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:Va2X3mrYQthvC7JygMXvSw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:iW34qsv8FmJjDDdZDm6ylw # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/EventType.pm b/lib/npg_tracking/Schema/Result/EventType.pm index da890846..f476829d 100644 --- a/lib/npg_tracking/Schema/Result/EventType.pm +++ b/lib/npg_tracking/Schema/Result/EventType.pm @@ -108,7 +108,7 @@ __PACKAGE__->belongs_to( "entity_type", "npg_tracking::Schema::Result::EntityType", { id_entity_type => "id_entity_type" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 events @@ -127,8 +127,8 @@ __PACKAGE__->has_many( ); -# Created by DBIx::Class::Schema::Loader v0.07046 @ 2017-03-29 16:56:34 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:zlzIuoXKksCuAnCVChRQlw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:bvmkevh1cn8gaCS0EruQ2Q # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/Instrument.pm b/lib/npg_tracking/Schema/Result/Instrument.pm index e69c9af1..1af54622 100644 --- a/lib/npg_tracking/Schema/Result/Instrument.pm +++ b/lib/npg_tracking/Schema/Result/Instrument.pm @@ -241,7 +241,7 @@ __PACKAGE__->belongs_to( "instrument_format", "npg_tracking::Schema::Result::InstrumentFormat", { id_instrument_format => "id_instrument_format" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument_mods @@ -290,8 +290,8 @@ __PACKAGE__->has_many( ); -# Created by DBIx::Class::Schema::Loader v0.07049 @ 2022-01-10 16:30:08 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7AZ9QOLc9VZulP3ExZljWQ +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:EZWWx8ih32aSy82wpKEPLQ # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentAnnotation.pm b/lib/npg_tracking/Schema/Result/InstrumentAnnotation.pm index 7b8fc9c5..061e23cf 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentAnnotation.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentAnnotation.pm @@ -115,7 +115,7 @@ __PACKAGE__->belongs_to( "annotation", "npg_tracking::Schema::Result::Annotation", { id_annotation => "id_annotation" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument @@ -130,12 +130,12 @@ __PACKAGE__->belongs_to( "instrument", "npg_tracking::Schema::Result::Instrument", { id_instrument => "id_instrument" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:42 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:+3wjXy3XATMRUrcKq5Q5Dw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:/xqdoyW0RURN6fnrCSzA1A # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentDesignation.pm b/lib/npg_tracking/Schema/Result/InstrumentDesignation.pm index a028fd64..0991cafb 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentDesignation.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentDesignation.pm @@ -111,7 +111,7 @@ __PACKAGE__->belongs_to( "designation", "npg_tracking::Schema::Result::Designation", { id_designation => "id_designation" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument @@ -126,12 +126,12 @@ __PACKAGE__->belongs_to( "instrument", "npg_tracking::Schema::Result::Instrument", { id_instrument => "id_instrument" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:42 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:75BtblGp9IlL23gHdPu74w +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:KHcCuo5jZz2lAyNyo5Kqyg # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentFormat.pm b/lib/npg_tracking/Schema/Result/InstrumentFormat.pm index d32a0089..036b7a20 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentFormat.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentFormat.pm @@ -189,7 +189,7 @@ __PACKAGE__->belongs_to( "manufacturer", "npg_tracking::Schema::Result::Manufacturer", { id_manufacturer => "id_manufacturer" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 runs @@ -208,8 +208,8 @@ __PACKAGE__->has_many( ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:42 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:65VhDik9vcGwGAJCX00ATg +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:esNDL3mLvW19/fKjWfsX/g # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentMod.pm b/lib/npg_tracking/Schema/Result/InstrumentMod.pm index 6ba938b5..67487060 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentMod.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentMod.pm @@ -167,7 +167,7 @@ __PACKAGE__->belongs_to( "instrument", "npg_tracking::Schema::Result::Instrument", { id_instrument => "id_instrument" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument_mod_dict @@ -182,7 +182,7 @@ __PACKAGE__->belongs_to( "instrument_mod_dict", "npg_tracking::Schema::Result::InstrumentModDict", { id_instrument_mod_dict => "id_instrument_mod_dict" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -197,12 +197,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:42 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:jx8LcIOopsROPJYpt927EQ +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HQKv7jeoJGBuxHmYHptWjg # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentStatus.pm b/lib/npg_tracking/Schema/Result/InstrumentStatus.pm index 2f31f08a..c4d14537 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentStatus.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentStatus.pm @@ -164,7 +164,7 @@ __PACKAGE__->belongs_to( "instrument", "npg_tracking::Schema::Result::Instrument", { id_instrument => "id_instrument" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument_status_annotations @@ -194,7 +194,7 @@ __PACKAGE__->belongs_to( "instrument_status_dict", "npg_tracking::Schema::Result::InstrumentStatusDict", { id_instrument_status_dict => "id_instrument_status_dict" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -209,12 +209,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:38 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:UzbBKhYHg31HV1VerPCvSw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:esGkAihro4/eSQRnoK9hfw # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentStatusAnnotation.pm b/lib/npg_tracking/Schema/Result/InstrumentStatusAnnotation.pm index c1cd35a7..7c728d0a 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentStatusAnnotation.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentStatusAnnotation.pm @@ -130,7 +130,7 @@ __PACKAGE__->belongs_to( "annotation", "npg_tracking::Schema::Result::Annotation", { id_annotation => "id_annotation" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument_status @@ -145,12 +145,12 @@ __PACKAGE__->belongs_to( "instrument_status", "npg_tracking::Schema::Result::InstrumentStatus", { id_instrument_status => "id_instrument_status" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:42 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:1Nry/5/Z7srL49QFt5725A +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:cJbTbXRF+P8weHj/iJAYqw # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/InstrumentUtilisation.pm b/lib/npg_tracking/Schema/Result/InstrumentUtilisation.pm index 4494b9b4..b5af0f96 100644 --- a/lib/npg_tracking/Schema/Result/InstrumentUtilisation.pm +++ b/lib/npg_tracking/Schema/Result/InstrumentUtilisation.pm @@ -259,12 +259,12 @@ __PACKAGE__->belongs_to( "instrument_format", "npg_tracking::Schema::Result::InstrumentFormat", { id_instrument_format => "id_instrument_format" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:42 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:XRcRHyyuFbfg8mml8Zazow +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:rbmVI5hlEgTZFDj665rTkw # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/Run.pm b/lib/npg_tracking/Schema/Result/Run.pm index 147fc8b9..ffc4327f 100644 --- a/lib/npg_tracking/Schema/Result/Run.pm +++ b/lib/npg_tracking/Schema/Result/Run.pm @@ -205,7 +205,7 @@ __PACKAGE__->belongs_to( "instrument", "npg_tracking::Schema::Result::Instrument", { id_instrument => "id_instrument" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 instrument_format @@ -220,7 +220,7 @@ __PACKAGE__->belongs_to( "instrument_format", "npg_tracking::Schema::Result::InstrumentFormat", { id_instrument_format => "id_instrument_format" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 run_annotations @@ -314,8 +314,8 @@ __PACKAGE__->has_many( ); -# Created by DBIx::Class::Schema::Loader v0.07046 @ 2017-03-29 17:02:05 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:T5Bt3yeyrr0HVBcwmlVzgA +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:CQYOGdpHICplAd+i+cHeUA # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/RunAnnotation.pm b/lib/npg_tracking/Schema/Result/RunAnnotation.pm index 22f0d084..7164223c 100644 --- a/lib/npg_tracking/Schema/Result/RunAnnotation.pm +++ b/lib/npg_tracking/Schema/Result/RunAnnotation.pm @@ -131,7 +131,7 @@ __PACKAGE__->belongs_to( "annotation", "npg_tracking::Schema::Result::Annotation", { id_annotation => "id_annotation" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 run @@ -146,12 +146,12 @@ __PACKAGE__->belongs_to( "run", "npg_tracking::Schema::Result::Run", { id_run => "id_run" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:43 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:CQlOPAhOvTlIY5xY8E07pw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:l7RDTNRRvgDHqX8hxdJlQA # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/RunLane.pm b/lib/npg_tracking/Schema/Result/RunLane.pm index 68710da2..e8e760fb 100644 --- a/lib/npg_tracking/Schema/Result/RunLane.pm +++ b/lib/npg_tracking/Schema/Result/RunLane.pm @@ -159,7 +159,7 @@ __PACKAGE__->belongs_to( "run", "npg_tracking::Schema::Result::Run", { id_run => "id_run" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 run_lane_annotations @@ -208,8 +208,8 @@ __PACKAGE__->has_many( ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2015-04-09 18:30:04 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:sx8IuqL2QoP14bT5pPCLHw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:r1nt5B+vzIvP6TfQpID2TA # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/RunLaneAnnotation.pm b/lib/npg_tracking/Schema/Result/RunLaneAnnotation.pm index f552a960..82712201 100644 --- a/lib/npg_tracking/Schema/Result/RunLaneAnnotation.pm +++ b/lib/npg_tracking/Schema/Result/RunLaneAnnotation.pm @@ -111,7 +111,7 @@ __PACKAGE__->belongs_to( "annotation", "npg_tracking::Schema::Result::Annotation", { id_annotation => "id_annotation" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 run_lane @@ -126,12 +126,12 @@ __PACKAGE__->belongs_to( "run_lane", "npg_tracking::Schema::Result::RunLane", { id_run_lane => "id_run_lane" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:43 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:uIpg3AS/VOzbk6wv3a2mjw +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:zSY29s221/qV7AsJvmk7HQ # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/RunLaneStatus.pm b/lib/npg_tracking/Schema/Result/RunLaneStatus.pm index 7dfd74cc..0c35e38b 100644 --- a/lib/npg_tracking/Schema/Result/RunLaneStatus.pm +++ b/lib/npg_tracking/Schema/Result/RunLaneStatus.pm @@ -151,7 +151,7 @@ __PACKAGE__->belongs_to( "run_lane", "npg_tracking::Schema::Result::RunLane", { id_run_lane => "id_run_lane" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 run_lane_status_dict @@ -166,7 +166,7 @@ __PACKAGE__->belongs_to( "run_lane_status_dict", "npg_tracking::Schema::Result::RunLaneStatusDict", { id_run_lane_status_dict => "id_run_lane_status_dict" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -181,12 +181,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:38 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:TkFv5J36/M51WwS1WQKs8Q +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:7J1yidKBoNfzfqgW3W45Lg # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/RunStatus.pm b/lib/npg_tracking/Schema/Result/RunStatus.pm index 4f877ede..f01ebc0b 100644 --- a/lib/npg_tracking/Schema/Result/RunStatus.pm +++ b/lib/npg_tracking/Schema/Result/RunStatus.pm @@ -143,7 +143,7 @@ __PACKAGE__->belongs_to( "run", "npg_tracking::Schema::Result::Run", { id_run => "id_run" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 run_status_dict @@ -158,7 +158,7 @@ __PACKAGE__->belongs_to( "run_status_dict", "npg_tracking::Schema::Result::RunStatusDict", { id_run_status_dict => "id_run_status_dict" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -173,12 +173,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:39 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:orIX7xdPPHiChilWRRZiUA +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:dT2INHDh66tlPrPsaEnGaA # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/StCache.pm b/lib/npg_tracking/Schema/Result/StCache.pm index 5a7a0f62..c68549c8 100644 --- a/lib/npg_tracking/Schema/Result/StCache.pm +++ b/lib/npg_tracking/Schema/Result/StCache.pm @@ -117,12 +117,12 @@ __PACKAGE__->belongs_to( "run", "npg_tracking::Schema::Result::Run", { id_run => "id_run" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:44 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:z94U+kHMmuqp4fmUf2A6RQ +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:WIckqgeVZpWwwqbDDY86eQ # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/TagFrequency.pm b/lib/npg_tracking/Schema/Result/TagFrequency.pm index f7e7dc7d..b4a2e1ab 100644 --- a/lib/npg_tracking/Schema/Result/TagFrequency.pm +++ b/lib/npg_tracking/Schema/Result/TagFrequency.pm @@ -129,7 +129,7 @@ __PACKAGE__->belongs_to( "entity_type", "npg_tracking::Schema::Result::EntityType", { id_entity_type => "id_entity_type" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 tag @@ -144,12 +144,12 @@ __PACKAGE__->belongs_to( "tag", "npg_tracking::Schema::Result::Tag", { id_tag => "id_tag" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07035 @ 2013-07-23 16:11:44 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:UaZohMSFyQuuGEd8Vu+6xg +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:QE2T1+guAvaGha1WhVHJpA # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/TagRun.pm b/lib/npg_tracking/Schema/Result/TagRun.pm index 61e5e63f..f3f55f2d 100644 --- a/lib/npg_tracking/Schema/Result/TagRun.pm +++ b/lib/npg_tracking/Schema/Result/TagRun.pm @@ -159,7 +159,7 @@ __PACKAGE__->belongs_to( "run", "npg_tracking::Schema::Result::Run", { id_run => "id_run" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 tag @@ -174,7 +174,7 @@ __PACKAGE__->belongs_to( "tag", "npg_tracking::Schema::Result::Tag", { id_tag => "id_tag" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -189,12 +189,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:39 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:HrDTfnZT1SczQAqIdC662Q +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:gwJTKwzEUkxDtXPWRDvjGg # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/TagRunLane.pm b/lib/npg_tracking/Schema/Result/TagRunLane.pm index e94fbd94..12f372f2 100644 --- a/lib/npg_tracking/Schema/Result/TagRunLane.pm +++ b/lib/npg_tracking/Schema/Result/TagRunLane.pm @@ -143,7 +143,7 @@ __PACKAGE__->belongs_to( "run_lane", "npg_tracking::Schema::Result::RunLane", { id_run_lane => "id_run_lane" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 tag @@ -158,7 +158,7 @@ __PACKAGE__->belongs_to( "tag", "npg_tracking::Schema::Result::Tag", { id_tag => "id_tag" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 user @@ -173,12 +173,12 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:39 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:vsGkeNEmY6ZJUVCDJYUL8w +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:rKipnwfKJTe2pzSiIwnQcA # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 diff --git a/lib/npg_tracking/Schema/Result/User2usergroup.pm b/lib/npg_tracking/Schema/Result/User2usergroup.pm index 012353fc..08bc65fd 100644 --- a/lib/npg_tracking/Schema/Result/User2usergroup.pm +++ b/lib/npg_tracking/Schema/Result/User2usergroup.pm @@ -121,7 +121,7 @@ __PACKAGE__->belongs_to( "user", "npg_tracking::Schema::Result::User", { id_user => "id_user" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); =head2 usergroup @@ -136,12 +136,12 @@ __PACKAGE__->belongs_to( "usergroup", "npg_tracking::Schema::Result::Usergroup", { id_usergroup => "id_usergroup" }, - { is_deferrable => 1, on_delete => "NO ACTION", on_update => "NO ACTION" }, + { is_deferrable => 1, on_delete => "RESTRICT", on_update => "RESTRICT" }, ); -# Created by DBIx::Class::Schema::Loader v0.07036 @ 2014-02-20 10:43:39 -# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:rDM3WmEbGffIzjPO9maIeA +# Created by DBIx::Class::Schema::Loader v0.07051 @ 2023-10-23 17:02:30 +# DO NOT MODIFY THIS OR ANYTHING ABOVE! md5sum:UmYTcDNpyGTSwfVphplsGQ # Author: david.jackson@sanger.ac.uk # Created: 2010-04-08 From fa60e2bc6f36cc907f09e0d4701f8e5c9b5f85ed Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 24 Oct 2023 09:12:15 +0100 Subject: [PATCH 11/35] Removed deprecated seq_qc_state method from st::api::lims --- lib/st/api/lims.pm | 26 -------------------------- 1 file changed, 26 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 2790c40e..47261d51 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -563,32 +563,6 @@ sub _build_required_insert_size { return $is_hash; } - -=head2 seq_qc_state - - 1 for passes, 0 for failed, undef if the value is not set. - - This method is deprecated as of 08 March 2016. It should not be used in any - new code. The only place where this method is used in production code is - the old warehouse loader. Deprecation warning is not appropriate because the - old wh loader logs will be flooded. - -=cut -sub seq_qc_state { - my $self = shift; - my $state = $self->driver ? $self->driver->qc_state : q[]; - if (!defined $state || $state eq '1' || $state eq '0') { - return $state; - } - if ($state eq q[]) { - return; - } - if (!exists $QC_EVAL_MAPPING{$state}) { - croak qq[Unexpected value '$state' for seq qc state in ] . $self->to_string; - } - return $QC_EVAL_MAPPING{$state}; -} - =head2 reference_genome Read-only accessor, not possible to set from the constructor. From 9b240ab10f6d567c3b93e7bada126f28989db7a7 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 24 Oct 2023 09:27:36 +0100 Subject: [PATCH 12/35] Removed deprecated methods for retrieving lims object descendants --- lib/npg_tracking/data/reference/find.pm | 4 ++-- lib/st/api/lims.pm | 25 ++----------------------- 2 files changed, 4 insertions(+), 25 deletions(-) diff --git a/lib/npg_tracking/data/reference/find.pm b/lib/npg_tracking/data/reference/find.pm index 11b9a380..2e96d48b 100644 --- a/lib/npg_tracking/data/reference/find.pm +++ b/lib/npg_tracking/data/reference/find.pm @@ -222,7 +222,7 @@ sub refs { $spiked_phix_index = $self->lims->spiked_phix_tag_index; } - my @alims = $self->lims->associated_lims; + my @alims = $self->lims->descendants; if (!@alims) { @alims = ($self->lims); } @@ -471,7 +471,7 @@ Marina Gourtovaia Emg8@sanger.ac.ukE =head1 LICENSE AND COPYRIGHT -Copyright (C) 2017 GRL +Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2023 Genome Research Ltd. This file is part of NPG. diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 47261d51..432d96eb 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -543,7 +543,7 @@ sub _build_required_insert_size { my $is_hash = {}; if (defined $self->position) { - my @alims = $self->associated_lims; + my @alims = $self->descendants; @alims = @alims ? @alims : ($self); foreach my $lims (@alims) { if ($lims->is_control) { @@ -1012,20 +1012,6 @@ sub descendants { return @lims; } -=head2 associated_lims - -The same as descendants. Retained for backward compatibility - -=cut -*associated_lims = \&descendants; #backward compat - -=head2 associated_child_lims - -The same as children. Retained for backward compatibility - -=cut -*associated_child_lims = \&children; #backward compat - =head2 children_ia Method providing fast (index-based) access to child lims object. @@ -1071,13 +1057,6 @@ sub sample_publishable_name { return $self->sample_accession_number() || $self->sample_public_name() || $self->sample_name(); } -=head2 associated_child_lims_ia - -The same as children_ia. Retained for backward compatibility - -=cut -*associated_child_lims_ia = \&children_ia; #backward compat - sub _list_of_attributes { my ($self, $attr_name, $with_spiked_control) = @_; my @l = (); @@ -1396,7 +1375,7 @@ Marina Gourtovaia Emg8@sanger.ac.ukE =head1 LICENSE AND COPYRIGHT -Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020,2021 Genome Research Ltd. +Copyright (C) 2013,2014,2015,2016,2017,2018,2019,2020,2021,2023 Genome Research Ltd. This file is part of NPG. From 2f26297759019a5dbd01f9908efd772278dc7c3b Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 24 Oct 2023 13:12:25 +0100 Subject: [PATCH 13/35] Dropped unused constants --- lib/st/api/lims.pm | 3 --- 1 file changed, 3 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 432d96eb..8b177b36 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -61,9 +61,6 @@ Readonly::Scalar our $CACHED_SAMPLESHEET_FILE_VAR_NAME => 'NPG_CACHED_SAMPLESHEE Readonly::Scalar my $SAMPLESHEET_DRIVER_TYPE => 'samplesheet'; Readonly::Scalar my $DEFAULT_DRIVER_TYPE => $SAMPLESHEET_DRIVER_TYPE; -Readonly::Scalar my $PROC_NAME_INDEX => 3; -Readonly::Hash my %QC_EVAL_MAPPING => {'pass' => 1, 'fail' => 0, 'pending' => undef, }; -Readonly::Scalar my $INLINE_INDEX_END => 10; Readonly::Scalar my $DUAL_INDEX_TAG_LENGTH => 16; Readonly::Hash my %METHODS_PER_CATEGORY => { From 723868a4498e30dec3f43beebfc4a7a06b8b2452 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 25 Oct 2023 15:50:22 +0100 Subject: [PATCH 14/35] Dropped lims accessors for which no data exist. Dropped project_id, project_name, request_id accessors from st::api::lims since this data is not represented in ml warehouse. project_ids method is dropped as well. --- lib/st/api/lims.pm | 17 +- t/40-st-lims.t | 2 +- t/data/samplesheet/4pool4libs_extended.csv | 224 +++++++++--------- t/data/samplesheet/6946_extended.csv | 28 +-- t/data/samplesheet/7007_extended.csv | 6 +- .../samplesheet/dual_index_extended_new.csv | 68 +++--- t/data/samplesheet/novaseq_multirun.csv | 20 +- 7 files changed, 175 insertions(+), 190 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 8b177b36..c72217f0 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -128,12 +128,7 @@ Readonly::Hash my %METHODS_PER_CATEGORY => { study_separate_y_chromosome_data /], - 'project' => [qw/ project_id - project_name - project_cost_code - /], - - 'request' => [qw/ request_id /], + 'project' => [qw/ project_cost_code /], }; Readonly::Array my @METHODS => sort map { @{$_} } values %METHODS_PER_CATEGORY; @@ -209,9 +204,6 @@ Readonly::Hash my %ATTRIBUTE_LIST_METHODS => { 'library' => [qw/ id name /], - 'project' => [qw/ id - - /], 'sample' => [qw/ accession_number cohort common_name @@ -1181,13 +1173,6 @@ Similar to study_names, but for study_titles. =cut -=head2 project_ids - -A list of project ids, similar to study_ids. - -=cut - - =head2 library_type Read-only accessor, not possible to set from the constructor. diff --git a/t/40-st-lims.t b/t/40-st-lims.t index cdc0a816..7d23e601 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -6,7 +6,7 @@ use Test::Warn; use File::Temp qw/ tempdir /; use Moose::Meta::Class; -my $num_delegated_methods = 48; +my $num_delegated_methods = 45; use_ok('st::api::lims'); diff --git a/t/data/samplesheet/4pool4libs_extended.csv b/t/data/samplesheet/4pool4libs_extended.csv index e7392dc6..87a7ad1b 100644 --- a/t/data/samplesheet/4pool4libs_extended.csv +++ b/t/data/samplesheet/4pool4libs_extended.csv @@ -1,112 +1,112 @@ -[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -1,7809257,ERS323818,,,,,No PCR,,,,,,,,0,0,8381746,0,7809257,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323818,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660679,,Hc_4_BC4_P2_5046_340285,Haemonchus contortus MHco3%2F4.BC4(P2)-5046,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, -2,7809258,ERS323819,,,,Fox bait,No PCR,,,,,,,,0,0,8381744,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, -3,7809258,ERS323819,,,,,No PCR,,,,,,,,0,0,8381745,0,7809258,Haemonchus contortus,6289,S0702,,,standard,,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, -4,8215019,ERS351213,,TAAGGCGA,TAGATCGC,,qPCR only,TAAGGCGATAGATCGC,,,,,,,0,0,8381739,0,8215019,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351213,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706390,,mES_ai2_s2_cell1,mES_ai2_s2_cell1,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,1, -4,8215020,ERS351214,,CGTACTAG,TAGATCGC,,qPCR only,CGTACTAGTAGATCGC,,,,,,,0,0,8381739,0,8215020,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351214,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706391,,mES_ai2_s2_cell2,mES_ai2_s2_cell2,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,2, -4,8215021,ERS351221,,AGGCAGAA,TAGATCGC,,qPCR only,AGGCAGAATAGATCGC,,,,,,,0,0,8381739,0,8215021,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351221,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706392,,mES_ai2_s2_cell3,mES_ai2_s2_cell3,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,3, -4,8215022,ERS351222,,TCCTGAGC,TAGATCGC,,qPCR only,TCCTGAGCTAGATCGC,,,,,,,0,0,8381739,0,8215022,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351222,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706393,,mES_ai2_s2_cell4,mES_ai2_s2_cell4,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,4, -4,8215023,ERS351223,,GGACTCCT,TAGATCGC,,qPCR only,GGACTCCTTAGATCGC,,,,,,,0,0,8381739,0,8215023,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351223,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706394,,mES_ai2_s2_cell5,mES_ai2_s2_cell5,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,5, -4,8215024,ERS351224,,TAGGCATG,TAGATCGC,,qPCR only,TAGGCATGTAGATCGC,,,,,,,0,0,8381739,0,8215024,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351224,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706395,,mES_ai2_s2_cell6,mES_ai2_s2_cell6,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,6, -4,8215025,ERS351225,,CTCTCTAC,TAGATCGC,,qPCR only,CTCTCTACTAGATCGC,,,,,,,0,0,8381739,0,8215025,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351225,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706396,,mES_ai2_s2_cell7,mES_ai2_s2_cell7,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,7, -4,8215026,ERS351218,,CAGAGAGG,TAGATCGC,,qPCR only,CAGAGAGGTAGATCGC,,,,,,,0,0,8381739,0,8215026,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351218,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706397,,mES_ai2_s2_cell8,mES_ai2_s2_cell8,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,8, -4,8215027,ERS351219,,GCTACGCT,TAGATCGC,,qPCR only,GCTACGCTTAGATCGC,,,,,,,0,0,8381739,0,8215027,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351219,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706398,,mES_ai2_s2_cell9,mES_ai2_s2_cell9,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,9, -4,8215028,ERS351220,,CGAGGCTG,TAGATCGC,,qPCR only,CGAGGCTGTAGATCGC,,,,,,,0,0,8381739,0,8215028,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351220,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706399,,mES_ai2_s2_cell10,mES_ai2_s2_cell10,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,10, -4,8215029,ERS351235,,AAGAGGCA,TAGATCGC,,qPCR only,AAGAGGCATAGATCGC,,,,,,,0,0,8381739,0,8215029,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351235,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706400,,mES_ai2_s2_cell11,mES_ai2_s2_cell11,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,11, -4,8215030,ERS351237,,GTAGAGGA,TAGATCGC,,qPCR only,GTAGAGGATAGATCGC,,,,,,,0,0,8381739,0,8215030,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351237,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706401,,mES_ai2_s2_cell12,mES_ai2_s2_cell12,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,12, -4,8215031,ERS351238,,TAAGGCGA,CTCTCTAT,,qPCR only,TAAGGCGACTCTCTAT,,,,,,,0,0,8381739,0,8215031,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351238,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706402,,mES_ai2_s2_cell13,mES_ai2_s2_cell13,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,13, -4,8215032,ERS351239,,CGTACTAG,CTCTCTAT,,qPCR only,CGTACTAGCTCTCTAT,,,,,,,0,0,8381739,0,8215032,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351239,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706403,,mES_ai2_s2_cell14,mES_ai2_s2_cell14,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,14, -4,8215033,ERS351241,,AGGCAGAA,CTCTCTAT,,qPCR only,AGGCAGAACTCTCTAT,,,,,,,0,0,8381739,0,8215033,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351241,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706404,,mES_ai2_s2_cell15,mES_ai2_s2_cell15,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,15, -4,8215034,ERS351226,,TCCTGAGC,CTCTCTAT,,qPCR only,TCCTGAGCCTCTCTAT,,,,,,,0,0,8381739,0,8215034,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351226,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706405,,mES_ai2_s2_cell16,mES_ai2_s2_cell16,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,16, -4,8215035,ERS351227,,GGACTCCT,CTCTCTAT,,qPCR only,GGACTCCTCTCTCTAT,,,,,,,0,0,8381739,0,8215035,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351227,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706406,,mES_ai2_s2_cell17,mES_ai2_s2_cell17,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,17, -4,8215036,ERS351234,,TAGGCATG,CTCTCTAT,,qPCR only,TAGGCATGCTCTCTAT,,,,,,,0,0,8381739,0,8215036,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351234,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706407,,mES_ai2_s2_cell18,mES_ai2_s2_cell18,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,18, -4,8215037,ERS351236,,CTCTCTAC,CTCTCTAT,,qPCR only,CTCTCTACCTCTCTAT,,,,,,,0,0,8381739,0,8215037,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351236,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706408,,mES_ai2_s2_cell19,mES_ai2_s2_cell19,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,19, -4,8215038,ERS351247,,CAGAGAGG,CTCTCTAT,,qPCR only,CAGAGAGGCTCTCTAT,,,,,,,0,0,8381739,0,8215038,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351247,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706409,,mES_ai2_s2_cell20,mES_ai2_s2_cell20,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,20, -4,8215039,ERS351249,,GCTACGCT,CTCTCTAT,,qPCR only,GCTACGCTCTCTCTAT,,,,,,,0,0,8381739,0,8215039,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351249,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706410,,mES_ai2_s2_cell21,mES_ai2_s2_cell21,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,21, -4,8215040,ERS351251,,CGAGGCTG,CTCTCTAT,,qPCR only,CGAGGCTGCTCTCTAT,,,,,,,0,0,8381739,0,8215040,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351251,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706411,,mES_ai2_s2_cell22,mES_ai2_s2_cell22,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,22, -4,8215041,ERS351252,,AAGAGGCA,CTCTCTAT,,qPCR only,AAGAGGCACTCTCTAT,,,,,,,0,0,8381739,0,8215041,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351252,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706412,,mES_ai2_s2_cell23,mES_ai2_s2_cell23,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,23, -4,8215042,ERS351242,,GTAGAGGA,CTCTCTAT,,qPCR only,GTAGAGGACTCTCTAT,,,,,,,0,0,8381739,0,8215042,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351242,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706413,,mES_ai2_s2_cell24,mES_ai2_s2_cell24,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,24, -4,8215043,ERS351243,,TAAGGCGA,TATCCTCT,,qPCR only,TAAGGCGATATCCTCT,,,,,,,0,0,8381739,0,8215043,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351243,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706414,,mES_ai2_s2_cell25,mES_ai2_s2_cell25,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,25, -4,8215044,ERS351244,,CGTACTAG,TATCCTCT,,qPCR only,CGTACTAGTATCCTCT,,,,,,,0,0,8381739,0,8215044,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351244,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706415,,mES_ai2_s2_cell26,mES_ai2_s2_cell26,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,26, -4,8215045,ERS351245,,AGGCAGAA,TATCCTCT,,qPCR only,AGGCAGAATATCCTCT,,,,,,,0,0,8381739,0,8215045,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351245,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706416,,mES_ai2_s2_cell27,mES_ai2_s2_cell27,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,27, -4,8215046,ERS351248,,TCCTGAGC,TATCCTCT,,qPCR only,TCCTGAGCTATCCTCT,,,,,,,0,0,8381739,0,8215046,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351248,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706417,,mES_ai2_s2_cell28,mES_ai2_s2_cell28,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,28, -4,8215047,ERS351250,,GGACTCCT,TATCCTCT,,qPCR only,GGACTCCTTATCCTCT,,,,,,,0,0,8381739,0,8215047,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351250,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706418,,mES_ai2_s2_cell29,mES_ai2_s2_cell29,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,29, -4,8215048,ERS351260,,TAGGCATG,TATCCTCT,,qPCR only,TAGGCATGTATCCTCT,,,,,,,0,0,8381739,0,8215048,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351260,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706419,,mES_ai2_s2_cell30,mES_ai2_s2_cell30,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,30, -4,8215049,ERS351261,,CTCTCTAC,TATCCTCT,,qPCR only,CTCTCTACTATCCTCT,,,,,,,0,0,8381739,0,8215049,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351261,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706420,,mES_ai2_s2_cell31,mES_ai2_s2_cell31,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,31, -4,8215050,ERS351254,,CAGAGAGG,TATCCTCT,,qPCR only,CAGAGAGGTATCCTCT,,,,,,,0,0,8381739,0,8215050,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351254,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706421,,mES_ai2_s2_cell32,mES_ai2_s2_cell32,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,32, -4,8215051,ERS351255,,GCTACGCT,TATCCTCT,,qPCR only,GCTACGCTTATCCTCT,,,,,,,0,0,8381739,0,8215051,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351255,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706422,,mES_ai2_s2_cell33,mES_ai2_s2_cell33,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,33, -4,8215052,ERS351256,,CGAGGCTG,TATCCTCT,,qPCR only,CGAGGCTGTATCCTCT,,,,,,,0,0,8381739,0,8215052,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351256,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706423,,mES_ai2_s2_cell34,mES_ai2_s2_cell34,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,34, -4,8215053,ERS351257,,AAGAGGCA,TATCCTCT,,qPCR only,AAGAGGCATATCCTCT,,,,,,,0,0,8381739,0,8215053,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351257,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706424,,mES_ai2_s2_cell35,mES_ai2_s2_cell35,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,35, -4,8215054,ERS351258,,GTAGAGGA,TATCCTCT,,qPCR only,GTAGAGGATATCCTCT,,,,,,,0,0,8381739,0,8215054,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351258,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706425,,mES_ai2_s2_cell36,mES_ai2_s2_cell36,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,36, -4,8215055,ERS351259,,TAAGGCGA,AGAGTAGA,,qPCR only,TAAGGCGAAGAGTAGA,,,,,,,0,0,8381739,0,8215055,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351259,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706426,,mES_ai2_s2_cell37,mES_ai2_s2_cell37,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,37, -4,8215056,ERS351269,,CGTACTAG,AGAGTAGA,,qPCR only,CGTACTAGAGAGTAGA,,,,,,,0,0,8381739,0,8215056,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351269,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706427,,mES_ai2_s2_cell38,mES_ai2_s2_cell38,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,38, -4,8215057,ERS351271,,AGGCAGAA,AGAGTAGA,,qPCR only,AGGCAGAAAGAGTAGA,,,,,,,0,0,8381739,0,8215057,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351271,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706428,,mES_ai2_s2_cell39,mES_ai2_s2_cell39,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,39, -4,8215058,ERS351262,,TCCTGAGC,AGAGTAGA,,qPCR only,TCCTGAGCAGAGTAGA,,,,,,,0,0,8381739,0,8215058,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351262,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706429,,mES_ai2_s2_cell40,mES_ai2_s2_cell40,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,40, -4,8215059,ERS351263,,GGACTCCT,AGAGTAGA,,qPCR only,GGACTCCTAGAGTAGA,,,,,,,0,0,8381739,0,8215059,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351263,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706430,,mES_ai2_s2_cell41,mES_ai2_s2_cell41,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,41, -4,8215060,ERS351264,,TAGGCATG,AGAGTAGA,,qPCR only,TAGGCATGAGAGTAGA,,,,,,,0,0,8381739,0,8215060,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351264,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706431,,mES_ai2_s2_cell42,mES_ai2_s2_cell42,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,42, -4,8215061,ERS351266,,CTCTCTAC,AGAGTAGA,,qPCR only,CTCTCTACAGAGTAGA,,,,,,,0,0,8381739,0,8215061,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351266,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706432,,mES_ai2_s2_cell43,mES_ai2_s2_cell43,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,43, -4,8215062,ERS351267,,CAGAGAGG,AGAGTAGA,,qPCR only,CAGAGAGGAGAGTAGA,,,,,,,0,0,8381739,0,8215062,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351267,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706433,,mES_ai2_s2_cell44,mES_ai2_s2_cell44,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,44, -4,8215063,ERS351268,,GCTACGCT,AGAGTAGA,,qPCR only,GCTACGCTAGAGTAGA,,,,,,,0,0,8381739,0,8215063,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351268,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706434,,mES_ai2_s2_cell45,mES_ai2_s2_cell45,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,45, -4,8215064,ERS351270,,CGAGGCTG,AGAGTAGA,,qPCR only,CGAGGCTGAGAGTAGA,,,,,,,0,0,8381739,0,8215064,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351270,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706435,,mES_ai2_s2_cell46,mES_ai2_s2_cell46,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,46, -4,8215065,ERS351272,,AAGAGGCA,AGAGTAGA,,qPCR only,AAGAGGCAAGAGTAGA,,,,,,,0,0,8381739,0,8215065,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351272,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706436,,mES_ai2_s2_cell47,mES_ai2_s2_cell47,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,47, -4,8215066,ERS351273,,GTAGAGGA,AGAGTAGA,,qPCR only,GTAGAGGAAGAGTAGA,,,,,,,0,0,8381739,0,8215066,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351273,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706437,,mES_ai2_s2_cell48,mES_ai2_s2_cell48,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,48, -4,8215067,ERS351275,,TAAGGCGA,GTAAGGAG,,qPCR only,TAAGGCGAGTAAGGAG,,,,,,,0,0,8381739,0,8215067,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351275,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706438,,mES_ai2_s2_cell49,mES_ai2_s2_cell49,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,49, -4,8215068,ERS351277,,CGTACTAG,GTAAGGAG,,qPCR only,CGTACTAGGTAAGGAG,,,,,,,0,0,8381739,0,8215068,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351277,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706439,,mES_ai2_s2_cell50,mES_ai2_s2_cell50,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,50, -4,8215069,ERS351278,,AGGCAGAA,GTAAGGAG,,qPCR only,AGGCAGAAGTAAGGAG,,,,,,,0,0,8381739,0,8215069,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351278,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706440,,mES_ai2_s2_cell51,mES_ai2_s2_cell51,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,51, -4,8215070,ERS351279,,TCCTGAGC,GTAAGGAG,,qPCR only,TCCTGAGCGTAAGGAG,,,,,,,0,0,8381739,0,8215070,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351279,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706441,,mES_ai2_s2_cell52,mES_ai2_s2_cell52,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,52, -4,8215071,ERS351280,,GGACTCCT,GTAAGGAG,,qPCR only,GGACTCCTGTAAGGAG,,,,,,,0,0,8381739,0,8215071,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351280,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706442,,mES_ai2_s2_cell53,mES_ai2_s2_cell53,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,53, -4,8215072,ERS351281,,TAGGCATG,GTAAGGAG,,qPCR only,TAGGCATGGTAAGGAG,,,,,,,0,0,8381739,0,8215072,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351281,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706443,,mES_ai2_s2_cell54,mES_ai2_s2_cell54,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,54, -4,8215073,ERS351282,,CTCTCTAC,GTAAGGAG,,qPCR only,CTCTCTACGTAAGGAG,,,,,,,0,0,8381739,0,8215073,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351282,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706444,,mES_ai2_s2_cell55,mES_ai2_s2_cell55,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,55, -4,8215074,ERS351274,,CAGAGAGG,GTAAGGAG,,qPCR only,CAGAGAGGGTAAGGAG,,,,,,,0,0,8381739,0,8215074,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351274,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706445,,mES_ai2_s2_cell56,mES_ai2_s2_cell56,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,56, -4,8215075,ERS351276,,GCTACGCT,GTAAGGAG,,qPCR only,GCTACGCTGTAAGGAG,,,,,,,0,0,8381739,0,8215075,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351276,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706446,,mES_ai2_s2_cell57,mES_ai2_s2_cell57,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,57, -4,8215076,ERS351285,,CGAGGCTG,GTAAGGAG,,qPCR only,CGAGGCTGGTAAGGAG,,,,,,,0,0,8381739,0,8215076,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351285,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706447,,mES_ai2_s2_cell58,mES_ai2_s2_cell58,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,58, -4,8215077,ERS351286,,AAGAGGCA,GTAAGGAG,,qPCR only,AAGAGGCAGTAAGGAG,,,,,,,0,0,8381739,0,8215077,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351286,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706448,,mES_ai2_s2_cell59,mES_ai2_s2_cell59,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,59, -4,8215078,ERS351287,,GTAGAGGA,GTAAGGAG,,qPCR only,GTAGAGGAGTAAGGAG,,,,,,,0,0,8381739,0,8215078,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351287,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706449,,mES_ai2_s2_cell60,mES_ai2_s2_cell60,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,60, -4,8215079,ERS351288,,TAAGGCGA,ACTGCATA,,qPCR only,TAAGGCGAACTGCATA,,,,,,,0,0,8381739,0,8215079,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351288,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706450,,mES_ai2_s2_cell61,mES_ai2_s2_cell61,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,61, -4,8215080,ERS351289,,CGTACTAG,ACTGCATA,,qPCR only,CGTACTAGACTGCATA,,,,,,,0,0,8381739,0,8215080,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351289,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706451,,mES_ai2_s2_cell62,mES_ai2_s2_cell62,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,62, -4,8215081,ERS351290,,AGGCAGAA,ACTGCATA,,qPCR only,AGGCAGAAACTGCATA,,,,,,,0,0,8381739,0,8215081,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351290,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706452,,mES_ai2_s2_cell63,mES_ai2_s2_cell63,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,63, -4,8215082,ERS351283,,TCCTGAGC,ACTGCATA,,qPCR only,TCCTGAGCACTGCATA,,,,,,,0,0,8381739,0,8215082,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351283,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706453,,mES_ai2_s2_cell64,mES_ai2_s2_cell64,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,64, -4,8215083,ERS351284,,GGACTCCT,ACTGCATA,,qPCR only,GGACTCCTACTGCATA,,,,,,,0,0,8381739,0,8215083,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351284,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706454,,mES_ai2_s2_cell65,mES_ai2_s2_cell65,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,65, -4,8215084,ERS351292,,TAGGCATG,ACTGCATA,,qPCR only,TAGGCATGACTGCATA,,,,,,,0,0,8381739,0,8215084,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351292,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706455,,mES_ai2_s2_cell66,mES_ai2_s2_cell66,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,66, -4,8215085,ERS351293,,CTCTCTAC,ACTGCATA,,qPCR only,CTCTCTACACTGCATA,,,,,,,0,0,8381739,0,8215085,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351293,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706456,,mES_ai2_s2_cell67,mES_ai2_s2_cell67,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,67, -4,8215086,ERS351294,,CAGAGAGG,ACTGCATA,,qPCR only,CAGAGAGGACTGCATA,,,,,,,0,0,8381739,0,8215086,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351294,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706457,,mES_ai2_s2_cell68,mES_ai2_s2_cell68,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,68, -4,8215087,ERS351295,,GCTACGCT,ACTGCATA,,qPCR only,GCTACGCTACTGCATA,,,,,,,0,0,8381739,0,8215087,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351295,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706458,,mES_ai2_s2_cell69,mES_ai2_s2_cell69,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,69, -4,8215088,ERS351296,,CGAGGCTG,ACTGCATA,,qPCR only,CGAGGCTGACTGCATA,,,,,,,0,0,8381739,0,8215088,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351296,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706459,,mES_ai2_s2_cell70,mES_ai2_s2_cell70,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,70, -4,8215089,ERS351297,,AAGAGGCA,ACTGCATA,,qPCR only,AAGAGGCAACTGCATA,,,,,,,0,0,8381739,0,8215089,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351297,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706460,,mES_ai2_s2_cell71,mES_ai2_s2_cell71,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,71, -4,8215090,ERS351291,,GTAGAGGA,ACTGCATA,,qPCR only,GTAGAGGAACTGCATA,,,,,,,0,0,8381739,0,8215090,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351291,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706461,,mES_ai2_s2_cell72,mES_ai2_s2_cell72,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,72, -4,8215091,ERS351299,,TAAGGCGA,AAGGAGTA,,qPCR only,TAAGGCGAAAGGAGTA,,,,,,,0,0,8381739,0,8215091,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351299,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706462,,mES_ai2_s2_cell73,mES_ai2_s2_cell73,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,73, -4,8215092,ERS351301,,CGTACTAG,AAGGAGTA,,qPCR only,CGTACTAGAAGGAGTA,,,,,,,0,0,8381739,0,8215092,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351301,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706463,,mES_ai2_s2_cell74,mES_ai2_s2_cell74,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,74, -4,8215093,ERS351302,,AGGCAGAA,AAGGAGTA,,qPCR only,AGGCAGAAAAGGAGTA,,,,,,,0,0,8381739,0,8215093,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351302,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706464,,mES_ai2_s2_cell75,mES_ai2_s2_cell75,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,75, -4,8215094,ERS351303,,TCCTGAGC,AAGGAGTA,,qPCR only,TCCTGAGCAAGGAGTA,,,,,,,0,0,8381739,0,8215094,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351303,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706465,,mES_ai2_s2_cell76,mES_ai2_s2_cell76,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,76, -4,8215095,ERS351304,,GGACTCCT,AAGGAGTA,,qPCR only,GGACTCCTAAGGAGTA,,,,,,,0,0,8381739,0,8215095,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351304,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706466,,mES_ai2_s2_cell77,mES_ai2_s2_cell77,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,77, -4,8215096,ERS351305,,TAGGCATG,AAGGAGTA,,qPCR only,TAGGCATGAAGGAGTA,,,,,,,0,0,8381739,0,8215096,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351305,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706467,,mES_ai2_s2_cell78,mES_ai2_s2_cell78,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,78, -4,8215097,ERS351306,,CTCTCTAC,AAGGAGTA,,qPCR only,CTCTCTACAAGGAGTA,,,,,,,0,0,8381739,0,8215097,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351306,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706468,,mES_ai2_s2_cell79,mES_ai2_s2_cell79,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,79, -4,8215098,ERS351298,,CAGAGAGG,AAGGAGTA,,qPCR only,CAGAGAGGAAGGAGTA,,,,,,,0,0,8381739,0,8215098,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351298,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706469,,mES_ai2_s2_cell80,mES_ai2_s2_cell80,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,80, -4,8215099,ERS351300,,GCTACGCT,AAGGAGTA,,qPCR only,GCTACGCTAAGGAGTA,,,,,,,0,0,8381739,0,8215099,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351300,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706470,,mES_ai2_s2_cell81,mES_ai2_s2_cell81,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,81, -4,8215100,ERS351309,,CGAGGCTG,AAGGAGTA,,qPCR only,CGAGGCTGAAGGAGTA,,,,,,,0,0,8381739,0,8215100,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351309,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706471,,mES_ai2_s2_cell82,mES_ai2_s2_cell82,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,82, -4,8215101,ERS351310,,AAGAGGCA,AAGGAGTA,,qPCR only,AAGAGGCAAAGGAGTA,,,,,,,0,0,8381739,0,8215101,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351310,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706472,,mES_ai2_s2_cell83,mES_ai2_s2_cell83,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,83, -4,8215102,ERS351311,,GTAGAGGA,AAGGAGTA,,qPCR only,GTAGAGGAAAGGAGTA,,,,,,,0,0,8381739,0,8215102,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351311,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706473,,mES_ai2_s2_cell84,mES_ai2_s2_cell84,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,84, -4,8215103,ERS351312,,TAAGGCGA,CTAAGCCT,,qPCR only,TAAGGCGACTAAGCCT,,,,,,,0,0,8381739,0,8215103,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351312,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706474,,mES_ai2_s2_cell85,mES_ai2_s2_cell85,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,85, -4,8215104,ERS351313,,CGTACTAG,CTAAGCCT,,qPCR only,CGTACTAGCTAAGCCT,,,,,,,0,0,8381739,0,8215104,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351313,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706475,,mES_ai2_s2_cell86,mES_ai2_s2_cell86,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,86, -4,8215105,ERS351314,,AGGCAGAA,CTAAGCCT,,qPCR only,AGGCAGAACTAAGCCT,,,,,,,0,0,8381739,0,8215105,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351314,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706476,,mES_ai2_s2_cell87,mES_ai2_s2_cell87,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,87, -4,8215106,ERS351307,,TCCTGAGC,CTAAGCCT,,qPCR only,TCCTGAGCCTAAGCCT,,,,,,,0,0,8381739,0,8215106,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351307,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706477,,mES_ai2_s2_cell88,mES_ai2_s2_cell88,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,88, -4,8215107,ERS351308,,GGACTCCT,CTAAGCCT,,qPCR only,GGACTCCTCTAAGCCT,,,,,,,0,0,8381739,0,8215107,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351308,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706478,,mES_ai2_s2_cell89,mES_ai2_s2_cell89,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,89, -4,8215108,ERS351315,,TAGGCATG,CTAAGCCT,,qPCR only,TAGGCATGCTAAGCCT,,,,,,,0,0,8381739,0,8215108,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351315,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706479,,mES_ai2_s2_cell90,mES_ai2_s2_cell90,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,90, -4,8215109,ERS351316,,CTCTCTAC,CTAAGCCT,,qPCR only,CTCTCTACCTAAGCCT,,,,,,,0,0,8381739,0,8215109,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351316,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706480,,mES_ai2_s2_cell91,mES_ai2_s2_cell91,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,91, -4,8215110,ERS351317,,CAGAGAGG,CTAAGCCT,,qPCR only,CAGAGAGGCTAAGCCT,,,,,,,0,0,8381739,0,8215110,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351317,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706481,,mES_ai2_s2_cell92,mES_ai2_s2_cell92,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,92, -4,8215111,ERS351318,,GCTACGCT,CTAAGCCT,,qPCR only,GCTACGCTCTAAGCCT,,,,,,,0,0,8381739,0,8215111,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351318,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706482,,mES_ai2_s2_cell93,mES_ai2_s2_cell93,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,93, -4,8215112,ERS351319,,CGAGGCTG,CTAAGCCT,,qPCR only,CGAGGCTGCTAAGCCT,,,,,,,0,0,8381739,0,8215112,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351319,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706483,,mES_ai2_s2_cell94,mES_ai2_s2_cell94,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,94, -4,8215113,ERS351320,,AAGAGGCA,CTAAGCCT,,qPCR only,AAGAGGCACTAAGCCT,,,,,,,0,0,8381739,0,8215113,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351320,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706484,,mES_ai2_s2_cell95,mES_ai2_s2_cell95,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,95, -4,8215114,ERS351321,,GTAGAGGA,CTAAGCCT,,qPCR only,GTAGAGGACTAAGCCT,,,,,,,0,0,8381739,0,8215114,mus musculus,10090,S0917,,,standard,,,from:300 to:1000,ERS351321,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706485,,mES_ai2_s2_cell96,mES_ai2_s2_cell96,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,96, -4,6200285,6946_4_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381739,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, -5,8269740,EGAN00001173643,,,,,No PCR,,,,,,,,0,0,8381740,0,8269740,Human,9606,S0814,,,standard,,,from:300 to:500,EGAN00001173643,,Homo sapiens,0,,,PD14393b,1712041,,PD14393b_wg,PD14393b,,,168,EGAS00001000290,1,0,0,Wholegenome libraries will be prepared.,2239,MPN Whole Genomes,Homo_sapiens (CGP_GRCh37.NCBI.allchr_MT),0,Myeloproliferative Disease Whole Genomes,, -6,8324592,ERS354532,,GAGATTCC,TAATCTTA,,Pre-quality controlled,GAGATTCCTAATCTTA,,,,,,,0,0,8381741,0,8324592,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354532,,Mus musculus,0,,RNA,,1694494,,T_BCM1_F4,RT_37,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,64, -6,8324593,ERS354533,,ATTCAGAA,TAATCTTA,,Pre-quality controlled,ATTCAGAATAATCTTA,,,,,,,0,0,8381741,0,8324593,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354533,,Mus musculus,0,,RNA,,1694495,,T_BCM1_F5,RT_38,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,65, -6,6200285,6946_6_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381741,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, -7,8324594,ERS354534,,GAGATTCC,CAGGACGT,,Pre-quality controlled,GAGATTCCCAGGACGT,,,,,,,0,0,8381742,0,8324594,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354534,,Mus musculus,0,,RNA,,1694496,,T_CBF1_G4,RT_39,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,76, -7,8324595,ERS354535,,ATTCAGAA,CAGGACGT,,Pre-quality controlled,ATTCAGAACAGGACGT,,,,,,,0,0,8381742,0,8324595,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354535,,Mus musculus,0,,RNA,,1694497,,T_CBF1_G5,RT_40,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,77, -7,6200285,6946_7_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381742,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, -8,8324596,ERS354536,,GAGATTCC,GTACTGAC,,Pre-quality controlled,GAGATTCCGTACTGAC,,,,,,,0,0,8381743,0,8324596,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354536,,Mus musculus,0,,RNA,,1694498,,T_CBM2_H4,RT_41,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,88, -8,8324597,ERS354537,,ATTCAGAA,GTACTGAC,,Pre-quality controlled,ATTCAGAAGTACTGAC,,,,,,,0,0,8381743,0,8324597,Mouse,10090,S1553,,,standard,,,from:100 to:1000,ERS354537,,Mus musculus,0,,RNA,,1694499,,T_CBM2_H5,RT_42,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,89, -8,6200285,6946_8_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381743,0,6200285,,,,,,standard,,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,purpose,qc_state,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,7809257,ERS323818,,,,,No PCR,,,,,,,,0,0,8381746,0,7809257,Haemonchus contortus,6289,S0702,standard,,from:400 to:550,ERS323818,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660679,,Hc_4_BC4_P2_5046_340285,Haemonchus contortus MHco3%2F4.BC4(P2)-5046,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +2,7809258,ERS323819,,,,Fox bait,No PCR,,,,,,,,0,0,8381744,0,7809258,Haemonchus contortus,6289,S0702,standard,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +3,7809258,ERS323819,,,,,No PCR,,,,,,,,0,0,8381745,0,7809258,Haemonchus contortus,6289,S0702,standard,,from:400 to:550,ERS323819,,Haemonchus contortus,0,,25-30 mixed male and female worms%2C strain identity was checked using a panel of 4 microsatellite loci that discriminate Haemonchus contortus strains,,1660680,,Hc_10_BC4_P2_5779_340285,Haemonchus contortus MHco3%2F10.BC4(P2)-5779,Haemonchus_contortus (V1_21June13),,168,ERP000430,0,0,0,Two H. contortus ivermectin resistance strains have been backcrossed.,1697,Haemonchus contortus Ivermectin Resistance, ,0,Haemonchus contortus Ivermectin Resistance,, +4,8215019,ERS351213,,TAAGGCGA,TAGATCGC,,qPCR only,TAAGGCGATAGATCGC,,,,,,,0,0,8381739,0,8215019,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351213,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706390,,mES_ai2_s2_cell1,mES_ai2_s2_cell1,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,1, +4,8215020,ERS351214,,CGTACTAG,TAGATCGC,,qPCR only,CGTACTAGTAGATCGC,,,,,,,0,0,8381739,0,8215020,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351214,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706391,,mES_ai2_s2_cell2,mES_ai2_s2_cell2,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,2, +4,8215021,ERS351221,,AGGCAGAA,TAGATCGC,,qPCR only,AGGCAGAATAGATCGC,,,,,,,0,0,8381739,0,8215021,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351221,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706392,,mES_ai2_s2_cell3,mES_ai2_s2_cell3,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,3, +4,8215022,ERS351222,,TCCTGAGC,TAGATCGC,,qPCR only,TCCTGAGCTAGATCGC,,,,,,,0,0,8381739,0,8215022,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351222,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706393,,mES_ai2_s2_cell4,mES_ai2_s2_cell4,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,4, +4,8215023,ERS351223,,GGACTCCT,TAGATCGC,,qPCR only,GGACTCCTTAGATCGC,,,,,,,0,0,8381739,0,8215023,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351223,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706394,,mES_ai2_s2_cell5,mES_ai2_s2_cell5,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,5, +4,8215024,ERS351224,,TAGGCATG,TAGATCGC,,qPCR only,TAGGCATGTAGATCGC,,,,,,,0,0,8381739,0,8215024,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351224,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706395,,mES_ai2_s2_cell6,mES_ai2_s2_cell6,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,6, +4,8215025,ERS351225,,CTCTCTAC,TAGATCGC,,qPCR only,CTCTCTACTAGATCGC,,,,,,,0,0,8381739,0,8215025,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351225,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706396,,mES_ai2_s2_cell7,mES_ai2_s2_cell7,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,7, +4,8215026,ERS351218,,CAGAGAGG,TAGATCGC,,qPCR only,CAGAGAGGTAGATCGC,,,,,,,0,0,8381739,0,8215026,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351218,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706397,,mES_ai2_s2_cell8,mES_ai2_s2_cell8,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,8, +4,8215027,ERS351219,,GCTACGCT,TAGATCGC,,qPCR only,GCTACGCTTAGATCGC,,,,,,,0,0,8381739,0,8215027,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351219,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706398,,mES_ai2_s2_cell9,mES_ai2_s2_cell9,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,9, +4,8215028,ERS351220,,CGAGGCTG,TAGATCGC,,qPCR only,CGAGGCTGTAGATCGC,,,,,,,0,0,8381739,0,8215028,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351220,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706399,,mES_ai2_s2_cell10,mES_ai2_s2_cell10,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,10, +4,8215029,ERS351235,,AAGAGGCA,TAGATCGC,,qPCR only,AAGAGGCATAGATCGC,,,,,,,0,0,8381739,0,8215029,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351235,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706400,,mES_ai2_s2_cell11,mES_ai2_s2_cell11,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,11, +4,8215030,ERS351237,,GTAGAGGA,TAGATCGC,,qPCR only,GTAGAGGATAGATCGC,,,,,,,0,0,8381739,0,8215030,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351237,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706401,,mES_ai2_s2_cell12,mES_ai2_s2_cell12,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,12, +4,8215031,ERS351238,,TAAGGCGA,CTCTCTAT,,qPCR only,TAAGGCGACTCTCTAT,,,,,,,0,0,8381739,0,8215031,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351238,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706402,,mES_ai2_s2_cell13,mES_ai2_s2_cell13,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,13, +4,8215032,ERS351239,,CGTACTAG,CTCTCTAT,,qPCR only,CGTACTAGCTCTCTAT,,,,,,,0,0,8381739,0,8215032,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351239,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706403,,mES_ai2_s2_cell14,mES_ai2_s2_cell14,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,14, +4,8215033,ERS351241,,AGGCAGAA,CTCTCTAT,,qPCR only,AGGCAGAACTCTCTAT,,,,,,,0,0,8381739,0,8215033,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351241,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706404,,mES_ai2_s2_cell15,mES_ai2_s2_cell15,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,15, +4,8215034,ERS351226,,TCCTGAGC,CTCTCTAT,,qPCR only,TCCTGAGCCTCTCTAT,,,,,,,0,0,8381739,0,8215034,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351226,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706405,,mES_ai2_s2_cell16,mES_ai2_s2_cell16,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,16, +4,8215035,ERS351227,,GGACTCCT,CTCTCTAT,,qPCR only,GGACTCCTCTCTCTAT,,,,,,,0,0,8381739,0,8215035,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351227,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706406,,mES_ai2_s2_cell17,mES_ai2_s2_cell17,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,17, +4,8215036,ERS351234,,TAGGCATG,CTCTCTAT,,qPCR only,TAGGCATGCTCTCTAT,,,,,,,0,0,8381739,0,8215036,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351234,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706407,,mES_ai2_s2_cell18,mES_ai2_s2_cell18,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,18, +4,8215037,ERS351236,,CTCTCTAC,CTCTCTAT,,qPCR only,CTCTCTACCTCTCTAT,,,,,,,0,0,8381739,0,8215037,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351236,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706408,,mES_ai2_s2_cell19,mES_ai2_s2_cell19,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,19, +4,8215038,ERS351247,,CAGAGAGG,CTCTCTAT,,qPCR only,CAGAGAGGCTCTCTAT,,,,,,,0,0,8381739,0,8215038,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351247,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706409,,mES_ai2_s2_cell20,mES_ai2_s2_cell20,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,20, +4,8215039,ERS351249,,GCTACGCT,CTCTCTAT,,qPCR only,GCTACGCTCTCTCTAT,,,,,,,0,0,8381739,0,8215039,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351249,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706410,,mES_ai2_s2_cell21,mES_ai2_s2_cell21,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,21, +4,8215040,ERS351251,,CGAGGCTG,CTCTCTAT,,qPCR only,CGAGGCTGCTCTCTAT,,,,,,,0,0,8381739,0,8215040,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351251,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706411,,mES_ai2_s2_cell22,mES_ai2_s2_cell22,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,22, +4,8215041,ERS351252,,AAGAGGCA,CTCTCTAT,,qPCR only,AAGAGGCACTCTCTAT,,,,,,,0,0,8381739,0,8215041,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351252,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706412,,mES_ai2_s2_cell23,mES_ai2_s2_cell23,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,23, +4,8215042,ERS351242,,GTAGAGGA,CTCTCTAT,,qPCR only,GTAGAGGACTCTCTAT,,,,,,,0,0,8381739,0,8215042,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351242,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706413,,mES_ai2_s2_cell24,mES_ai2_s2_cell24,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,24, +4,8215043,ERS351243,,TAAGGCGA,TATCCTCT,,qPCR only,TAAGGCGATATCCTCT,,,,,,,0,0,8381739,0,8215043,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351243,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706414,,mES_ai2_s2_cell25,mES_ai2_s2_cell25,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,25, +4,8215044,ERS351244,,CGTACTAG,TATCCTCT,,qPCR only,CGTACTAGTATCCTCT,,,,,,,0,0,8381739,0,8215044,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351244,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706415,,mES_ai2_s2_cell26,mES_ai2_s2_cell26,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,26, +4,8215045,ERS351245,,AGGCAGAA,TATCCTCT,,qPCR only,AGGCAGAATATCCTCT,,,,,,,0,0,8381739,0,8215045,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351245,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706416,,mES_ai2_s2_cell27,mES_ai2_s2_cell27,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,27, +4,8215046,ERS351248,,TCCTGAGC,TATCCTCT,,qPCR only,TCCTGAGCTATCCTCT,,,,,,,0,0,8381739,0,8215046,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351248,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706417,,mES_ai2_s2_cell28,mES_ai2_s2_cell28,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,28, +4,8215047,ERS351250,,GGACTCCT,TATCCTCT,,qPCR only,GGACTCCTTATCCTCT,,,,,,,0,0,8381739,0,8215047,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351250,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706418,,mES_ai2_s2_cell29,mES_ai2_s2_cell29,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,29, +4,8215048,ERS351260,,TAGGCATG,TATCCTCT,,qPCR only,TAGGCATGTATCCTCT,,,,,,,0,0,8381739,0,8215048,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351260,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706419,,mES_ai2_s2_cell30,mES_ai2_s2_cell30,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,30, +4,8215049,ERS351261,,CTCTCTAC,TATCCTCT,,qPCR only,CTCTCTACTATCCTCT,,,,,,,0,0,8381739,0,8215049,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351261,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706420,,mES_ai2_s2_cell31,mES_ai2_s2_cell31,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,31, +4,8215050,ERS351254,,CAGAGAGG,TATCCTCT,,qPCR only,CAGAGAGGTATCCTCT,,,,,,,0,0,8381739,0,8215050,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351254,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706421,,mES_ai2_s2_cell32,mES_ai2_s2_cell32,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,32, +4,8215051,ERS351255,,GCTACGCT,TATCCTCT,,qPCR only,GCTACGCTTATCCTCT,,,,,,,0,0,8381739,0,8215051,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351255,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706422,,mES_ai2_s2_cell33,mES_ai2_s2_cell33,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,33, +4,8215052,ERS351256,,CGAGGCTG,TATCCTCT,,qPCR only,CGAGGCTGTATCCTCT,,,,,,,0,0,8381739,0,8215052,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351256,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706423,,mES_ai2_s2_cell34,mES_ai2_s2_cell34,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,34, +4,8215053,ERS351257,,AAGAGGCA,TATCCTCT,,qPCR only,AAGAGGCATATCCTCT,,,,,,,0,0,8381739,0,8215053,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351257,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706424,,mES_ai2_s2_cell35,mES_ai2_s2_cell35,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,35, +4,8215054,ERS351258,,GTAGAGGA,TATCCTCT,,qPCR only,GTAGAGGATATCCTCT,,,,,,,0,0,8381739,0,8215054,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351258,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706425,,mES_ai2_s2_cell36,mES_ai2_s2_cell36,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,36, +4,8215055,ERS351259,,TAAGGCGA,AGAGTAGA,,qPCR only,TAAGGCGAAGAGTAGA,,,,,,,0,0,8381739,0,8215055,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351259,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706426,,mES_ai2_s2_cell37,mES_ai2_s2_cell37,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,37, +4,8215056,ERS351269,,CGTACTAG,AGAGTAGA,,qPCR only,CGTACTAGAGAGTAGA,,,,,,,0,0,8381739,0,8215056,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351269,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706427,,mES_ai2_s2_cell38,mES_ai2_s2_cell38,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,38, +4,8215057,ERS351271,,AGGCAGAA,AGAGTAGA,,qPCR only,AGGCAGAAAGAGTAGA,,,,,,,0,0,8381739,0,8215057,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351271,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706428,,mES_ai2_s2_cell39,mES_ai2_s2_cell39,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,39, +4,8215058,ERS351262,,TCCTGAGC,AGAGTAGA,,qPCR only,TCCTGAGCAGAGTAGA,,,,,,,0,0,8381739,0,8215058,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351262,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706429,,mES_ai2_s2_cell40,mES_ai2_s2_cell40,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,40, +4,8215059,ERS351263,,GGACTCCT,AGAGTAGA,,qPCR only,GGACTCCTAGAGTAGA,,,,,,,0,0,8381739,0,8215059,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351263,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706430,,mES_ai2_s2_cell41,mES_ai2_s2_cell41,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,41, +4,8215060,ERS351264,,TAGGCATG,AGAGTAGA,,qPCR only,TAGGCATGAGAGTAGA,,,,,,,0,0,8381739,0,8215060,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351264,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706431,,mES_ai2_s2_cell42,mES_ai2_s2_cell42,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,42, +4,8215061,ERS351266,,CTCTCTAC,AGAGTAGA,,qPCR only,CTCTCTACAGAGTAGA,,,,,,,0,0,8381739,0,8215061,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351266,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706432,,mES_ai2_s2_cell43,mES_ai2_s2_cell43,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,43, +4,8215062,ERS351267,,CAGAGAGG,AGAGTAGA,,qPCR only,CAGAGAGGAGAGTAGA,,,,,,,0,0,8381739,0,8215062,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351267,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706433,,mES_ai2_s2_cell44,mES_ai2_s2_cell44,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,44, +4,8215063,ERS351268,,GCTACGCT,AGAGTAGA,,qPCR only,GCTACGCTAGAGTAGA,,,,,,,0,0,8381739,0,8215063,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351268,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706434,,mES_ai2_s2_cell45,mES_ai2_s2_cell45,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,45, +4,8215064,ERS351270,,CGAGGCTG,AGAGTAGA,,qPCR only,CGAGGCTGAGAGTAGA,,,,,,,0,0,8381739,0,8215064,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351270,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706435,,mES_ai2_s2_cell46,mES_ai2_s2_cell46,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,46, +4,8215065,ERS351272,,AAGAGGCA,AGAGTAGA,,qPCR only,AAGAGGCAAGAGTAGA,,,,,,,0,0,8381739,0,8215065,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351272,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706436,,mES_ai2_s2_cell47,mES_ai2_s2_cell47,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,47, +4,8215066,ERS351273,,GTAGAGGA,AGAGTAGA,,qPCR only,GTAGAGGAAGAGTAGA,,,,,,,0,0,8381739,0,8215066,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351273,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706437,,mES_ai2_s2_cell48,mES_ai2_s2_cell48,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,48, +4,8215067,ERS351275,,TAAGGCGA,GTAAGGAG,,qPCR only,TAAGGCGAGTAAGGAG,,,,,,,0,0,8381739,0,8215067,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351275,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706438,,mES_ai2_s2_cell49,mES_ai2_s2_cell49,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,49, +4,8215068,ERS351277,,CGTACTAG,GTAAGGAG,,qPCR only,CGTACTAGGTAAGGAG,,,,,,,0,0,8381739,0,8215068,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351277,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706439,,mES_ai2_s2_cell50,mES_ai2_s2_cell50,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,50, +4,8215069,ERS351278,,AGGCAGAA,GTAAGGAG,,qPCR only,AGGCAGAAGTAAGGAG,,,,,,,0,0,8381739,0,8215069,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351278,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706440,,mES_ai2_s2_cell51,mES_ai2_s2_cell51,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,51, +4,8215070,ERS351279,,TCCTGAGC,GTAAGGAG,,qPCR only,TCCTGAGCGTAAGGAG,,,,,,,0,0,8381739,0,8215070,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351279,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706441,,mES_ai2_s2_cell52,mES_ai2_s2_cell52,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,52, +4,8215071,ERS351280,,GGACTCCT,GTAAGGAG,,qPCR only,GGACTCCTGTAAGGAG,,,,,,,0,0,8381739,0,8215071,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351280,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706442,,mES_ai2_s2_cell53,mES_ai2_s2_cell53,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,53, +4,8215072,ERS351281,,TAGGCATG,GTAAGGAG,,qPCR only,TAGGCATGGTAAGGAG,,,,,,,0,0,8381739,0,8215072,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351281,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706443,,mES_ai2_s2_cell54,mES_ai2_s2_cell54,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,54, +4,8215073,ERS351282,,CTCTCTAC,GTAAGGAG,,qPCR only,CTCTCTACGTAAGGAG,,,,,,,0,0,8381739,0,8215073,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351282,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706444,,mES_ai2_s2_cell55,mES_ai2_s2_cell55,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,55, +4,8215074,ERS351274,,CAGAGAGG,GTAAGGAG,,qPCR only,CAGAGAGGGTAAGGAG,,,,,,,0,0,8381739,0,8215074,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351274,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706445,,mES_ai2_s2_cell56,mES_ai2_s2_cell56,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,56, +4,8215075,ERS351276,,GCTACGCT,GTAAGGAG,,qPCR only,GCTACGCTGTAAGGAG,,,,,,,0,0,8381739,0,8215075,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351276,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706446,,mES_ai2_s2_cell57,mES_ai2_s2_cell57,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,57, +4,8215076,ERS351285,,CGAGGCTG,GTAAGGAG,,qPCR only,CGAGGCTGGTAAGGAG,,,,,,,0,0,8381739,0,8215076,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351285,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706447,,mES_ai2_s2_cell58,mES_ai2_s2_cell58,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,58, +4,8215077,ERS351286,,AAGAGGCA,GTAAGGAG,,qPCR only,AAGAGGCAGTAAGGAG,,,,,,,0,0,8381739,0,8215077,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351286,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706448,,mES_ai2_s2_cell59,mES_ai2_s2_cell59,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,59, +4,8215078,ERS351287,,GTAGAGGA,GTAAGGAG,,qPCR only,GTAGAGGAGTAAGGAG,,,,,,,0,0,8381739,0,8215078,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351287,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706449,,mES_ai2_s2_cell60,mES_ai2_s2_cell60,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,60, +4,8215079,ERS351288,,TAAGGCGA,ACTGCATA,,qPCR only,TAAGGCGAACTGCATA,,,,,,,0,0,8381739,0,8215079,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351288,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706450,,mES_ai2_s2_cell61,mES_ai2_s2_cell61,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,61, +4,8215080,ERS351289,,CGTACTAG,ACTGCATA,,qPCR only,CGTACTAGACTGCATA,,,,,,,0,0,8381739,0,8215080,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351289,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706451,,mES_ai2_s2_cell62,mES_ai2_s2_cell62,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,62, +4,8215081,ERS351290,,AGGCAGAA,ACTGCATA,,qPCR only,AGGCAGAAACTGCATA,,,,,,,0,0,8381739,0,8215081,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351290,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706452,,mES_ai2_s2_cell63,mES_ai2_s2_cell63,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,63, +4,8215082,ERS351283,,TCCTGAGC,ACTGCATA,,qPCR only,TCCTGAGCACTGCATA,,,,,,,0,0,8381739,0,8215082,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351283,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706453,,mES_ai2_s2_cell64,mES_ai2_s2_cell64,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,64, +4,8215083,ERS351284,,GGACTCCT,ACTGCATA,,qPCR only,GGACTCCTACTGCATA,,,,,,,0,0,8381739,0,8215083,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351284,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706454,,mES_ai2_s2_cell65,mES_ai2_s2_cell65,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,65, +4,8215084,ERS351292,,TAGGCATG,ACTGCATA,,qPCR only,TAGGCATGACTGCATA,,,,,,,0,0,8381739,0,8215084,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351292,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706455,,mES_ai2_s2_cell66,mES_ai2_s2_cell66,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,66, +4,8215085,ERS351293,,CTCTCTAC,ACTGCATA,,qPCR only,CTCTCTACACTGCATA,,,,,,,0,0,8381739,0,8215085,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351293,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706456,,mES_ai2_s2_cell67,mES_ai2_s2_cell67,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,67, +4,8215086,ERS351294,,CAGAGAGG,ACTGCATA,,qPCR only,CAGAGAGGACTGCATA,,,,,,,0,0,8381739,0,8215086,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351294,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706457,,mES_ai2_s2_cell68,mES_ai2_s2_cell68,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,68, +4,8215087,ERS351295,,GCTACGCT,ACTGCATA,,qPCR only,GCTACGCTACTGCATA,,,,,,,0,0,8381739,0,8215087,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351295,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706458,,mES_ai2_s2_cell69,mES_ai2_s2_cell69,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,69, +4,8215088,ERS351296,,CGAGGCTG,ACTGCATA,,qPCR only,CGAGGCTGACTGCATA,,,,,,,0,0,8381739,0,8215088,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351296,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706459,,mES_ai2_s2_cell70,mES_ai2_s2_cell70,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,70, +4,8215089,ERS351297,,AAGAGGCA,ACTGCATA,,qPCR only,AAGAGGCAACTGCATA,,,,,,,0,0,8381739,0,8215089,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351297,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706460,,mES_ai2_s2_cell71,mES_ai2_s2_cell71,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,71, +4,8215090,ERS351291,,GTAGAGGA,ACTGCATA,,qPCR only,GTAGAGGAACTGCATA,,,,,,,0,0,8381739,0,8215090,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351291,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706461,,mES_ai2_s2_cell72,mES_ai2_s2_cell72,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,72, +4,8215091,ERS351299,,TAAGGCGA,AAGGAGTA,,qPCR only,TAAGGCGAAAGGAGTA,,,,,,,0,0,8381739,0,8215091,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351299,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706462,,mES_ai2_s2_cell73,mES_ai2_s2_cell73,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,73, +4,8215092,ERS351301,,CGTACTAG,AAGGAGTA,,qPCR only,CGTACTAGAAGGAGTA,,,,,,,0,0,8381739,0,8215092,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351301,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706463,,mES_ai2_s2_cell74,mES_ai2_s2_cell74,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,74, +4,8215093,ERS351302,,AGGCAGAA,AAGGAGTA,,qPCR only,AGGCAGAAAAGGAGTA,,,,,,,0,0,8381739,0,8215093,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351302,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706464,,mES_ai2_s2_cell75,mES_ai2_s2_cell75,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,75, +4,8215094,ERS351303,,TCCTGAGC,AAGGAGTA,,qPCR only,TCCTGAGCAAGGAGTA,,,,,,,0,0,8381739,0,8215094,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351303,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706465,,mES_ai2_s2_cell76,mES_ai2_s2_cell76,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,76, +4,8215095,ERS351304,,GGACTCCT,AAGGAGTA,,qPCR only,GGACTCCTAAGGAGTA,,,,,,,0,0,8381739,0,8215095,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351304,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706466,,mES_ai2_s2_cell77,mES_ai2_s2_cell77,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,77, +4,8215096,ERS351305,,TAGGCATG,AAGGAGTA,,qPCR only,TAGGCATGAAGGAGTA,,,,,,,0,0,8381739,0,8215096,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351305,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706467,,mES_ai2_s2_cell78,mES_ai2_s2_cell78,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,78, +4,8215097,ERS351306,,CTCTCTAC,AAGGAGTA,,qPCR only,CTCTCTACAAGGAGTA,,,,,,,0,0,8381739,0,8215097,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351306,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706468,,mES_ai2_s2_cell79,mES_ai2_s2_cell79,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,79, +4,8215098,ERS351298,,CAGAGAGG,AAGGAGTA,,qPCR only,CAGAGAGGAAGGAGTA,,,,,,,0,0,8381739,0,8215098,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351298,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706469,,mES_ai2_s2_cell80,mES_ai2_s2_cell80,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,80, +4,8215099,ERS351300,,GCTACGCT,AAGGAGTA,,qPCR only,GCTACGCTAAGGAGTA,,,,,,,0,0,8381739,0,8215099,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351300,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706470,,mES_ai2_s2_cell81,mES_ai2_s2_cell81,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,81, +4,8215100,ERS351309,,CGAGGCTG,AAGGAGTA,,qPCR only,CGAGGCTGAAGGAGTA,,,,,,,0,0,8381739,0,8215100,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351309,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706471,,mES_ai2_s2_cell82,mES_ai2_s2_cell82,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,82, +4,8215101,ERS351310,,AAGAGGCA,AAGGAGTA,,qPCR only,AAGAGGCAAAGGAGTA,,,,,,,0,0,8381739,0,8215101,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351310,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706472,,mES_ai2_s2_cell83,mES_ai2_s2_cell83,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,83, +4,8215102,ERS351311,,GTAGAGGA,AAGGAGTA,,qPCR only,GTAGAGGAAAGGAGTA,,,,,,,0,0,8381739,0,8215102,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351311,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706473,,mES_ai2_s2_cell84,mES_ai2_s2_cell84,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,84, +4,8215103,ERS351312,,TAAGGCGA,CTAAGCCT,,qPCR only,TAAGGCGACTAAGCCT,,,,,,,0,0,8381739,0,8215103,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351312,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706474,,mES_ai2_s2_cell85,mES_ai2_s2_cell85,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,85, +4,8215104,ERS351313,,CGTACTAG,CTAAGCCT,,qPCR only,CGTACTAGCTAAGCCT,,,,,,,0,0,8381739,0,8215104,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351313,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706475,,mES_ai2_s2_cell86,mES_ai2_s2_cell86,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,86, +4,8215105,ERS351314,,AGGCAGAA,CTAAGCCT,,qPCR only,AGGCAGAACTAAGCCT,,,,,,,0,0,8381739,0,8215105,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351314,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706476,,mES_ai2_s2_cell87,mES_ai2_s2_cell87,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,87, +4,8215106,ERS351307,,TCCTGAGC,CTAAGCCT,,qPCR only,TCCTGAGCCTAAGCCT,,,,,,,0,0,8381739,0,8215106,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351307,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706477,,mES_ai2_s2_cell88,mES_ai2_s2_cell88,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,88, +4,8215107,ERS351308,,GGACTCCT,CTAAGCCT,,qPCR only,GGACTCCTCTAAGCCT,,,,,,,0,0,8381739,0,8215107,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351308,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706478,,mES_ai2_s2_cell89,mES_ai2_s2_cell89,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,89, +4,8215108,ERS351315,,TAGGCATG,CTAAGCCT,,qPCR only,TAGGCATGCTAAGCCT,,,,,,,0,0,8381739,0,8215108,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351315,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706479,,mES_ai2_s2_cell90,mES_ai2_s2_cell90,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,90, +4,8215109,ERS351316,,CTCTCTAC,CTAAGCCT,,qPCR only,CTCTCTACCTAAGCCT,,,,,,,0,0,8381739,0,8215109,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351316,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706480,,mES_ai2_s2_cell91,mES_ai2_s2_cell91,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,91, +4,8215110,ERS351317,,CAGAGAGG,CTAAGCCT,,qPCR only,CAGAGAGGCTAAGCCT,,,,,,,0,0,8381739,0,8215110,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351317,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706481,,mES_ai2_s2_cell92,mES_ai2_s2_cell92,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,92, +4,8215111,ERS351318,,GCTACGCT,CTAAGCCT,,qPCR only,GCTACGCTCTAAGCCT,,,,,,,0,0,8381739,0,8215111,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351318,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706482,,mES_ai2_s2_cell93,mES_ai2_s2_cell93,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,93, +4,8215112,ERS351319,,CGAGGCTG,CTAAGCCT,,qPCR only,CGAGGCTGCTAAGCCT,,,,,,,0,0,8381739,0,8215112,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351319,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706483,,mES_ai2_s2_cell94,mES_ai2_s2_cell94,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,94, +4,8215113,ERS351320,,AAGAGGCA,CTAAGCCT,,qPCR only,AAGAGGCACTAAGCCT,,,,,,,0,0,8381739,0,8215113,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351320,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706484,,mES_ai2_s2_cell95,mES_ai2_s2_cell95,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,95, +4,8215114,ERS351321,,GTAGAGGA,CTAAGCCT,,qPCR only,GTAGAGGACTAAGCCT,,,,,,,0,0,8381739,0,8215114,mus musculus,10090,S0917,standard,,from:300 to:1000,ERS351321,,Mus Musculus,0,,mRNAseq Nextera library made from G4 ES cell line from a male blastocyst from a C57BL%2F6Ncr male x 129S6%2FSvEvTac female,,1706485,,mES_ai2_s2_cell96,mES_ai2_s2_cell96,Mus_musculus (NCBIm37),,168,ERP003293,1,0,0,This study aims to investigate%0D%0A,2658,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency,Mus_musculus (NCBIm37),0,Single-cell analysis of the transcriptomic heterogeneity of ground state pluripotency ,96, +4,6200285,6946_4_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381739,0,6200285,,,,standard,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +5,8269740,EGAN00001173643,,,,,No PCR,,,,,,,,0,0,8381740,0,8269740,Human,9606,S0814,standard,,from:300 to:500,EGAN00001173643,,Homo sapiens,0,,,PD14393b,1712041,,PD14393b_wg,PD14393b,,,168,EGAS00001000290,1,0,0,Wholegenome libraries will be prepared.,2239,MPN Whole Genomes,Homo_sapiens (CGP_GRCh37.NCBI.allchr_MT),0,Myeloproliferative Disease Whole Genomes,, +6,8324592,ERS354532,,GAGATTCC,TAATCTTA,,Pre-quality controlled,GAGATTCCTAATCTTA,,,,,,,0,0,8381741,0,8324592,Mouse,10090,S1553,standard,,from:100 to:1000,ERS354532,,Mus musculus,0,,RNA,,1694494,,T_BCM1_F4,RT_37,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,64, +6,8324593,ERS354533,,ATTCAGAA,TAATCTTA,,Pre-quality controlled,ATTCAGAATAATCTTA,,,,,,,0,0,8381741,0,8324593,Mouse,10090,S1553,standard,,from:100 to:1000,ERS354533,,Mus musculus,0,,RNA,,1694495,,T_BCM1_F5,RT_38,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,65, +6,6200285,6946_6_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381741,0,6200285,,,,standard,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +7,8324594,ERS354534,,GAGATTCC,CAGGACGT,,Pre-quality controlled,GAGATTCCCAGGACGT,,,,,,,0,0,8381742,0,8324594,Mouse,10090,S1553,standard,,from:100 to:1000,ERS354534,,Mus musculus,0,,RNA,,1694496,,T_CBF1_G4,RT_39,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,76, +7,8324595,ERS354535,,ATTCAGAA,CAGGACGT,,Pre-quality controlled,ATTCAGAACAGGACGT,,,,,,,0,0,8381742,0,8324595,Mouse,10090,S1553,standard,,from:100 to:1000,ERS354535,,Mus musculus,0,,RNA,,1694497,,T_CBF1_G5,RT_40,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,77, +7,6200285,6946_7_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381742,0,6200285,,,,standard,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, +8,8324596,ERS354536,,GAGATTCC,GTACTGAC,,Pre-quality controlled,GAGATTCCGTACTGAC,,,,,,,0,0,8381743,0,8324596,Mouse,10090,S1553,standard,,from:100 to:1000,ERS354536,,Mus musculus,0,,RNA,,1694498,,T_CBM2_H4,RT_41,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,88, +8,8324597,ERS354537,,ATTCAGAA,GTACTGAC,,Pre-quality controlled,ATTCAGAAGTACTGAC,,,,,,,0,0,8381743,0,8324597,Mouse,10090,S1553,standard,,from:100 to:1000,ERS354537,,Mus musculus,0,,RNA,,1694499,,T_CBM2_H5,RT_42,,,168,ERP002223,1,0,0,In order to examine the impact of genetic variation on epigenetic marking and control of gene expression.,2501,Mouse model to quantify genotype-epigenotype variations_RNA,Mus_musculus (GRCm38),0,Mouse model to quantify genotype-epigenotype variations ,89, +8,6200285,6946_8_ACAACGCAAT,,ACAACGCAAT,,,,ACAACGCAAT,,,,,,,1,0,8381743,0,6200285,,,,standard,,,,,,,,,,,,,,,,168,,1,0,0,None,198,Illumina Controls, ,0,,168, diff --git a/t/data/samplesheet/6946_extended.csv b/t/data/samplesheet/6946_extended.csv index bfd0b845..b2522a74 100644 --- a/t/data/samplesheet/6946_extended.csv +++ b/t/data/samplesheet/6946_extended.csv @@ -1,14 +1,14 @@ -[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -Sample_ID,Sample_Name,GenomeFolder,Index,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -3789278,Salmonella pullorum,,ATCACGTT,,Standard,ATCACGTT,,,,,,,0,0,3789299,0,3789278,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289832,,sp200shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,1, -3789279,Bordetella Pertussis,,CGATGTTT,,Standard,CGATGTTT,,,,,,,0,0,3789299,0,3789279,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289833,,bp200shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,2, -3789280,Plasmodium Falciparum,,TTAGGCAT,,Standard,TTAGGCAT,,,,,,,0,0,3789299,0,3789280,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289834,,3D7200shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,3, -3789281,Homo sapiens,,TGACCACT,,Standard,TGACCACT,,,,,,,0,0,3789299,0,3789281,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,1,,genomic DNA,,1289835,,human200shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,4, -3789282,Salmonella pullorum,,ACAGTGGT,,Standard,ACAGTGGT,,,,,,,0,0,3789299,0,3789282,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289836,,sp300shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,5, -3789283,Bordetella Pertussis,,GCCAATGT,,Standard,GCCAATGT,,,,,,,0,0,3789299,0,3789283,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289837,,bp300shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,6, -3789284,Plasmodium Falciparum,,CAGATCTG,,Standard,CAGATCTG,,,,,,,0,0,3789299,0,3789284,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289838,,3D7300shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,7, -3789285,Homo sapiens,,ACTTGATG,,Standard,ACTTGATG,,,,,,,0,0,3789299,0,3789285,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289839,,human300shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,8, -3789286,Salmonella pullorum,,GATCAGCG,,Standard,GATCAGCG,,,,,,,0,0,3789299,0,3789286,Salmonella pullorum,590,S0696,,,standard,,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289840,,sp400shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,9, -3789287,Bordetella Pertussis,,TAGCTTGT,,Standard,TAGCTTGT,,,,,,,0,0,3789299,0,3789287,Bordetella Pertussis,520,S0696,,,standard,,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289841,,bp400shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,10, -3789288,Plasmodium Falciparum,,GGCTACAG,,Standard,GGCTACAG,,,,,,,0,0,3789299,0,3789288,Plasmodium Falciparum,5820,S0696,,,standard,,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289842,,3D7400shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,11, -3789289,Homo sapiens,,CTTGTACT,,Standard,CTTGTACT,,,,,,,0,0,3789299,0,3789289,Homo sapiens,9606,S0696,,,standard,,,from:200 to:700,,,Human,0,,genomic DNA,,1289843,,human400shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,12, +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Sample_ID,Sample_Name,GenomeFolder,Index,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,purpose,qc_state,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +3789278,Salmonella pullorum,,ATCACGTT,,Standard,ATCACGTT,,,,,,,0,0,3789299,0,3789278,Salmonella pullorum,590,S0696,standard,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289832,,sp200shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,1, +3789279,Bordetella Pertussis,,CGATGTTT,,Standard,CGATGTTT,,,,,,,0,0,3789299,0,3789279,Bordetella Pertussis,520,S0696,standard,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289833,,bp200shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,2, +3789280,Plasmodium Falciparum,,TTAGGCAT,,Standard,TTAGGCAT,,,,,,,0,0,3789299,0,3789280,Plasmodium Falciparum,5820,S0696,standard,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289834,,3D7200shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,3, +3789281,Homo sapiens,,TGACCACT,,Standard,TGACCACT,,,,,,,0,0,3789299,0,3789281,Homo sapiens,9606,S0696,standard,,from:200 to:700,,,Human,1,,genomic DNA,,1289835,,human200shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,4, +3789282,Salmonella pullorum,,ACAGTGGT,,Standard,ACAGTGGT,,,,,,,0,0,3789299,0,3789282,Salmonella pullorum,590,S0696,standard,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289836,,sp300shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,5, +3789283,Bordetella Pertussis,,GCCAATGT,,Standard,GCCAATGT,,,,,,,0,0,3789299,0,3789283,Bordetella Pertussis,520,S0696,standard,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289837,,bp300shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,6, +3789284,Plasmodium Falciparum,,CAGATCTG,,Standard,CAGATCTG,,,,,,,0,0,3789299,0,3789284,Plasmodium Falciparum,5820,S0696,standard,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289838,,3D7300shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,7, +3789285,Homo sapiens,,ACTTGATG,,Standard,ACTTGATG,,,,,,,0,0,3789299,0,3789285,Homo sapiens,9606,S0696,standard,,from:200 to:700,,,Human,0,,genomic DNA,,1289839,,human300shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,8, +3789286,Salmonella pullorum,,GATCAGCG,,Standard,GATCAGCG,,,,,,,0,0,3789299,0,3789286,Salmonella pullorum,590,S0696,standard,,from:200 to:700,,,Salmonella pullorum,0,,genomic DNA,,1289840,,sp400shear,Salmonella pullorum,Salmonella_pullorum (449_87),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,9, +3789287,Bordetella Pertussis,,TAGCTTGT,,Standard,TAGCTTGT,,,,,,,0,0,3789299,0,3789287,Bordetella Pertussis,520,S0696,standard,,from:200 to:700,,,Bordetella Pertussis,0,,genomic DNA,,1289841,,bp400shear,Bordetella Pertussis,Bordetella_pertussis (ST24),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,10, +3789288,Plasmodium Falciparum,,GGCTACAG,,Standard,GGCTACAG,,,,,,,0,0,3789299,0,3789288,Plasmodium Falciparum,5820,S0696,standard,,from:200 to:700,,,Plasmodium Falciparum,0,,genomic DNA,,1289842,,3D7400shear,Plasmodium Falciparum,Plasmodium_falciparum (3D7),,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,11, +3789289,Homo sapiens,,CTTGTACT,,Standard,CTTGTACT,,,,,,,0,0,3789299,0,3789289,Homo sapiens,9606,S0696,standard,,from:200 to:700,,,Human,0,,genomic DNA,,1289843,,human400shear,Homo sapiens,Homo_sapiens (GRCh37_53) DO_NOT_USE,,,,1,1,1,I have agreed to alpha test the kapa hifi qPCR kit.,700,Kapa HiFi test, ,1,hifi test,12, diff --git a/t/data/samplesheet/7007_extended.csv b/t/data/samplesheet/7007_extended.csv index df0f87c3..b50c7eaf 100644 --- a/t/data/samplesheet/7007_extended.csv +++ b/t/data/samplesheet/7007_extended.csv @@ -1,3 +1,3 @@ -[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -3789277,ERS092590,,,qPCR only,,,,,,,,0,0,3911772,0,3789277,Strongyloides ratti,34506,S0702,,,standard,,,from:300 to:400,ERS092590,,Strongyloides ratti,0,,,,1289830,,SriL3_66K_212889,Strongyloides ratti,Strongyloides_ratti (20100601),,,ERP001672,1,0,0,Strongyloides ratti is a common gastro-intestinal parasite of the rat.,521,Strongyloides ratti transcriptomics, ,0,Transcriptome sequencing of Strongyloides ratti,, +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,purpose,qc_state,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +3789277,ERS092590,,,qPCR only,,,,,,,,0,0,3911772,0,3789277,Strongyloides ratti,34506,S0702,standard,,from:300 to:400,ERS092590,,Strongyloides ratti,0,,,,1289830,,SriL3_66K_212889,Strongyloides ratti,Strongyloides_ratti (20100601),,,ERP001672,1,0,0,Strongyloides ratti is a common gastro-intestinal parasite of the rat.,521,Strongyloides ratti transcriptomics, ,0,Transcriptome sequencing of Strongyloides ratti,, diff --git a/t/data/samplesheet/dual_index_extended_new.csv b/t/data/samplesheet/dual_index_extended_new.csv index aa3e3f8c..e90b52e0 100644 --- a/t/data/samplesheet/dual_index_extended_new.csv +++ b/t/data/samplesheet/dual_index_extended_new.csv @@ -1,34 +1,34 @@ -[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -27037064,EGAN00002490956,,CGTGACAC,TTATTGCG,,Standard,CGTGACAC,TTATTGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037064,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490956,Normal,Homo sapiens,0,,,PD41305k_99,4396647,,6133STDY8786628,PD41305k_99,,PD41305k_99,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,1, -27037100,EGAN00002490958,,ACTTAGAG,CTCCATAA,,Standard,ACTTAGAG,CTCCATAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037100,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490958,Normal,Homo sapiens,0,,,PD41305k_102,4396650,,6133STDY8786631,PD41305k_102,,PD41305k_102,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,2, -27037112,EGAN00002490960,,TCAGGAAA,CCAAACCC,,Standard,TCAGGAAA,CCAAACCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037112,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490960,Normal,Homo sapiens,0,,,PD41305k_103,4396651,,6133STDY8786632,PD41305k_103,,PD41305k_103,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,3, -27037089,EGAN00002490966,,CGTCACCA,CTTGTTAA,,Standard,CGTCACCA,CTTGTTAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037089,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490966,Normal,Homo sapiens,0,,,PD41305k_109,4396657,,6133STDY8786638,PD41305k_109,,PD41305k_109,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,4, -27037101,EGAN00002490967,,GTGTTTCT,AAAGTGCG,,Standard,GTGTTTCT,AAAGTGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037101,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490967,Normal,Homo sapiens,0,,,PD41305k_110,4396658,,6133STDY8786639,PD41305k_110,,PD41305k_110,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,5, -27037113,EGAN00002490968,,GGCACTCA,AAGTACAG,,Standard,GGCACTCA,AAGTACAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037113,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490968,Normal,Homo sapiens,0,,,PD41305k_111,4396659,,6133STDY8786640,PD41305k_111,,PD41305k_111,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,6, -27037125,EGAN00002490970,,GTCATCTT,GCGCGCTA,,Standard,GTCATCTT,GCGCGCTA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037125,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490970,Normal,Homo sapiens,0,,,PD41305k_112,4396660,,6133STDY8786641,PD41305k_112,,PD41305k_112,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,7, -27037090,EGAN00002490973,,AGAGCTTA,TATAAAGC,,Standard,AGAGCTTA,TATAAAGC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037090,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490973,Normal,Homo sapiens,0,,,PD41305k_117,4396665,,6133STDY8786646,PD41305k_117,,PD41305k_117,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,8, -27037114,EGAN00002490976,,CTAAGTCC,TATCAAAG,,Standard,CTAAGTCC,TATCAAAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037114,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490976,Normal,Homo sapiens,0,,,PD41305k_119,4396667,,6133STDY8786648,PD41305k_119,,PD41305k_119,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,9, -27037091,EGAN00002490982,,GATCTTGA,GTCCCGCA,,Standard,GATCTTGA,GTCCCGCA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037091,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490982,Normal,Homo sapiens,0,,,PD41305k_125,4396673,,6133STDY8786654,PD41305k_125,,PD41305k_125,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,10, -27037056,EGAN00002491016,,GCGACTGA,CGCTTCAC,,Standard,GCGACTGA,CGCTTCAC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037056,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491016,Normal,Homo sapiens,0,,,PD41305k_130,4396678,,6133STDY8786659,PD41305k_130,,PD41305k_130,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,11, -27037104,EGAN00002491020,,TCCGGATT,CACAAGGA,,Standard,TCCGGATT,CACAAGGA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037104,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491020,Normal,Homo sapiens,0,,,PD41305k_134,4396682,,6133STDY8786663,PD41305k_134,,PD41305k_134,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,12, -27037129,EGAN00002491021,,AACGACTG,GAAATTAT,,Standard,AACGACTG,GAAATTAT,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037129,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491021,Normal,Homo sapiens,0,,,PD41305k_136,4396684,,6133STDY8786665,PD41305k_136,,PD41305k_136,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,13, -27037105,EGAN00002491029,,CTCGTGTC,TAGAGATA,,Standard,CTCGTGTC,TAGAGATA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037105,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491029,Normal,Homo sapiens,0,,,PD41305k_142,4396690,,6133STDY8786671,PD41305k_142,,PD41305k_142,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,14, -27037117,EGAN00002491028,,TGGCGGTC,AGCGTATT,,Standard,TGGCGGTC,AGCGTATT,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037117,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491028,Normal,Homo sapiens,0,,,PD41305k_143,4396691,,6133STDY8786672,PD41305k_143,,PD41305k_143,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,15, -27037058,EGAN00002491033,,TGATTTCC,ACTTCCGA,,Standard,TGATTTCC,ACTTCCGA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037058,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491033,Normal,Homo sapiens,0,,,PD41305k_146,4396694,,6133STDY8786675,PD41305k_146,,PD41305k_146,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,16, -27037094,EGAN00002491035,,TTTAAATG,ACGTTTAA,,Standard,TTTAAATG,ACGTTTAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037094,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491035,Normal,Homo sapiens,0,,,PD41305k_149,4396697,,6133STDY8786678,PD41305k_149,,PD41305k_149,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,17, -27037106,EGAN00002491037,,ACCTGCGG,ACGCCGCG,,Standard,ACCTGCGG,ACGCCGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037106,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491037,Normal,Homo sapiens,0,,,PD41305k_150,4396698,,6133STDY8786679,PD41305k_150,,PD41305k_150,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,18, -27037047,EGAN00002491039,,GACCGCAG,GGTCCCTC,,Standard,GACCGCAG,GGTCCCTC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037047,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491039,Normal,Homo sapiens,0,,,PD41305k_153,4396701,,6133STDY8786682,PD41305k_153,,PD41305k_153,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,19, -27037071,EGAN00002491041,,GTTTCATG,CAAACAAA,,Standard,GTTTCATG,CAAACAAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037071,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491041,Normal,Homo sapiens,0,,,PD41305k_155,4396703,,6133STDY8786684,PD41305k_155,,PD41305k_155,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,20, -27037083,EGAN00002491042,,AAACATCG,ACCAAAGC,,Standard,AAACATCG,ACCAAAGC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037083,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491042,Normal,Homo sapiens,0,,,PD41305k_156,4396704,,6133STDY8786685,PD41305k_156,,PD41305k_156,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,21, -27037048,EGAN00002491047,,GCTGCGCT,CCGATAAA,,Standard,GCTGCGCT,CCGATAAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037048,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491047,Normal,Homo sapiens,0,,,PD41305k_161,4396709,,6133STDY8786690,PD41305k_161,,PD41305k_161,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,22, -27037072,EGAN00002491048,,TGTCAGCT,CGCCGCCC,,Standard,TGTCAGCT,CGCCGCCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037072,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491048,Normal,Homo sapiens,0,,,PD41305k_163,4396711,,6133STDY8786692,PD41305k_163,,PD41305k_163,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,23, -27037084,EGAN00002490985,,CTCTCCGG,TGCCGGCA,,Standard,CTCTCCGG,TGCCGGCA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037084,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490985,Normal,Homo sapiens,0,,,PD41305k_164,4396712,,6133STDY8786693,PD41305k_164,,PD41305k_164,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,24, -27037134,EGAN00002490989,,AGAGTTAC,GATGGCTA,,Standard,AGAGTTAC,GATGGCTA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037134,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490989,Normal,Homo sapiens,0,,,PD41305k_168,4396716,,6133STDY8786697,PD41305k_168,,PD41305k_168,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,25, -27037061,EGAN00002490991,,CTCTTTAT,AAGCTCCG,,Standard,CTCTTTAT,AAGCTCCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037061,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490991,Normal,Homo sapiens,0,,,PD41305k_170,4396718,,6133STDY8786699,PD41305k_170,,PD41305k_170,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,26, -27037073,EGAN00002490992,,AGAGAGCC,ATAGGCAA,,Standard,AGAGAGCC,ATAGGCAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037073,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490992,Normal,Homo sapiens,0,,,PD41305k_171,4396719,,6133STDY8786700,PD41305k_171,,PD41305k_171,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,27, -27037085,EGAN00002490993,,CATCCACT,CCGGTGCC,,Standard,CATCCACT,CCGGTGCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037085,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002490993,Normal,Homo sapiens,0,,,PD41305k_172,4396720,,6133STDY8786701,PD41305k_172,,PD41305k_172,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,28, -27037086,EGAN00002491001,,CATTCTTC,TAACCGCG,,Standard,CATTCTTC,TAACCGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037086,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491001,Normal,Homo sapiens,0,,,PD41305k_180,4396728,,6133STDY8786709,PD41305k_180,,PD41305k_180,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,29, -27037098,EGAN00002491002,,CTCGACGT,GAAGAGCC,,Standard,CTCGACGT,GAAGAGCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037098,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491002,Normal,Homo sapiens,0,,,PD41305k_181,4396729,,6133STDY8786710,PD41305k_181,,PD41305k_181,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,30, -27037110,EGAN00002491003,,AGTTGCAA,ATCCTGAG,,Standard,AGTTGCAA,ATCCTGAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037110,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491003,Normal,Homo sapiens,0,,,PD41305k_182,4396730,,6133STDY8786711,PD41305k_182,,PD41305k_182,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,31, -27037051,EGAN00002491009,,GTAAGATG,AAAGGCTG,,Standard,GTAAGATG,AAAGGCTG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037051,,9606,S4360,,,standard,,,from:450 to:450,EGAN00002491009,Normal,Homo sapiens,0,,,PD41305k_185,4396733,,6133STDY8786714,PD41305k_185,,PD41305k_185,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,32, +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,purpose,qc_state,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +27037064,EGAN00002490956,,CGTGACAC,TTATTGCG,,Standard,CGTGACAC,TTATTGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037064,,9606,S4360,standard,,from:450 to:450,EGAN00002490956,Normal,Homo sapiens,0,,,PD41305k_99,4396647,,6133STDY8786628,PD41305k_99,,PD41305k_99,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,1, +27037100,EGAN00002490958,,ACTTAGAG,CTCCATAA,,Standard,ACTTAGAG,CTCCATAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037100,,9606,S4360,standard,,from:450 to:450,EGAN00002490958,Normal,Homo sapiens,0,,,PD41305k_102,4396650,,6133STDY8786631,PD41305k_102,,PD41305k_102,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,2, +27037112,EGAN00002490960,,TCAGGAAA,CCAAACCC,,Standard,TCAGGAAA,CCAAACCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037112,,9606,S4360,standard,,from:450 to:450,EGAN00002490960,Normal,Homo sapiens,0,,,PD41305k_103,4396651,,6133STDY8786632,PD41305k_103,,PD41305k_103,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,3, +27037089,EGAN00002490966,,CGTCACCA,CTTGTTAA,,Standard,CGTCACCA,CTTGTTAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037089,,9606,S4360,standard,,from:450 to:450,EGAN00002490966,Normal,Homo sapiens,0,,,PD41305k_109,4396657,,6133STDY8786638,PD41305k_109,,PD41305k_109,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,4, +27037101,EGAN00002490967,,GTGTTTCT,AAAGTGCG,,Standard,GTGTTTCT,AAAGTGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037101,,9606,S4360,standard,,from:450 to:450,EGAN00002490967,Normal,Homo sapiens,0,,,PD41305k_110,4396658,,6133STDY8786639,PD41305k_110,,PD41305k_110,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,5, +27037113,EGAN00002490968,,GGCACTCA,AAGTACAG,,Standard,GGCACTCA,AAGTACAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037113,,9606,S4360,standard,,from:450 to:450,EGAN00002490968,Normal,Homo sapiens,0,,,PD41305k_111,4396659,,6133STDY8786640,PD41305k_111,,PD41305k_111,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,6, +27037125,EGAN00002490970,,GTCATCTT,GCGCGCTA,,Standard,GTCATCTT,GCGCGCTA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037125,,9606,S4360,standard,,from:450 to:450,EGAN00002490970,Normal,Homo sapiens,0,,,PD41305k_112,4396660,,6133STDY8786641,PD41305k_112,,PD41305k_112,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,7, +27037090,EGAN00002490973,,AGAGCTTA,TATAAAGC,,Standard,AGAGCTTA,TATAAAGC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037090,,9606,S4360,standard,,from:450 to:450,EGAN00002490973,Normal,Homo sapiens,0,,,PD41305k_117,4396665,,6133STDY8786646,PD41305k_117,,PD41305k_117,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,8, +27037114,EGAN00002490976,,CTAAGTCC,TATCAAAG,,Standard,CTAAGTCC,TATCAAAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037114,,9606,S4360,standard,,from:450 to:450,EGAN00002490976,Normal,Homo sapiens,0,,,PD41305k_119,4396667,,6133STDY8786648,PD41305k_119,,PD41305k_119,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,9, +27037091,EGAN00002490982,,GATCTTGA,GTCCCGCA,,Standard,GATCTTGA,GTCCCGCA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037091,,9606,S4360,standard,,from:450 to:450,EGAN00002490982,Normal,Homo sapiens,0,,,PD41305k_125,4396673,,6133STDY8786654,PD41305k_125,,PD41305k_125,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,10, +27037056,EGAN00002491016,,GCGACTGA,CGCTTCAC,,Standard,GCGACTGA,CGCTTCAC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037056,,9606,S4360,standard,,from:450 to:450,EGAN00002491016,Normal,Homo sapiens,0,,,PD41305k_130,4396678,,6133STDY8786659,PD41305k_130,,PD41305k_130,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,11, +27037104,EGAN00002491020,,TCCGGATT,CACAAGGA,,Standard,TCCGGATT,CACAAGGA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037104,,9606,S4360,standard,,from:450 to:450,EGAN00002491020,Normal,Homo sapiens,0,,,PD41305k_134,4396682,,6133STDY8786663,PD41305k_134,,PD41305k_134,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,12, +27037129,EGAN00002491021,,AACGACTG,GAAATTAT,,Standard,AACGACTG,GAAATTAT,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037129,,9606,S4360,standard,,from:450 to:450,EGAN00002491021,Normal,Homo sapiens,0,,,PD41305k_136,4396684,,6133STDY8786665,PD41305k_136,,PD41305k_136,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,13, +27037105,EGAN00002491029,,CTCGTGTC,TAGAGATA,,Standard,CTCGTGTC,TAGAGATA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037105,,9606,S4360,standard,,from:450 to:450,EGAN00002491029,Normal,Homo sapiens,0,,,PD41305k_142,4396690,,6133STDY8786671,PD41305k_142,,PD41305k_142,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,14, +27037117,EGAN00002491028,,TGGCGGTC,AGCGTATT,,Standard,TGGCGGTC,AGCGTATT,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037117,,9606,S4360,standard,,from:450 to:450,EGAN00002491028,Normal,Homo sapiens,0,,,PD41305k_143,4396691,,6133STDY8786672,PD41305k_143,,PD41305k_143,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,15, +27037058,EGAN00002491033,,TGATTTCC,ACTTCCGA,,Standard,TGATTTCC,ACTTCCGA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037058,,9606,S4360,standard,,from:450 to:450,EGAN00002491033,Normal,Homo sapiens,0,,,PD41305k_146,4396694,,6133STDY8786675,PD41305k_146,,PD41305k_146,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,16, +27037094,EGAN00002491035,,TTTAAATG,ACGTTTAA,,Standard,TTTAAATG,ACGTTTAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037094,,9606,S4360,standard,,from:450 to:450,EGAN00002491035,Normal,Homo sapiens,0,,,PD41305k_149,4396697,,6133STDY8786678,PD41305k_149,,PD41305k_149,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,17, +27037106,EGAN00002491037,,ACCTGCGG,ACGCCGCG,,Standard,ACCTGCGG,ACGCCGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037106,,9606,S4360,standard,,from:450 to:450,EGAN00002491037,Normal,Homo sapiens,0,,,PD41305k_150,4396698,,6133STDY8786679,PD41305k_150,,PD41305k_150,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,18, +27037047,EGAN00002491039,,GACCGCAG,GGTCCCTC,,Standard,GACCGCAG,GGTCCCTC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037047,,9606,S4360,standard,,from:450 to:450,EGAN00002491039,Normal,Homo sapiens,0,,,PD41305k_153,4396701,,6133STDY8786682,PD41305k_153,,PD41305k_153,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,19, +27037071,EGAN00002491041,,GTTTCATG,CAAACAAA,,Standard,GTTTCATG,CAAACAAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037071,,9606,S4360,standard,,from:450 to:450,EGAN00002491041,Normal,Homo sapiens,0,,,PD41305k_155,4396703,,6133STDY8786684,PD41305k_155,,PD41305k_155,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,20, +27037083,EGAN00002491042,,AAACATCG,ACCAAAGC,,Standard,AAACATCG,ACCAAAGC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037083,,9606,S4360,standard,,from:450 to:450,EGAN00002491042,Normal,Homo sapiens,0,,,PD41305k_156,4396704,,6133STDY8786685,PD41305k_156,,PD41305k_156,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,21, +27037048,EGAN00002491047,,GCTGCGCT,CCGATAAA,,Standard,GCTGCGCT,CCGATAAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037048,,9606,S4360,standard,,from:450 to:450,EGAN00002491047,Normal,Homo sapiens,0,,,PD41305k_161,4396709,,6133STDY8786690,PD41305k_161,,PD41305k_161,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,22, +27037072,EGAN00002491048,,TGTCAGCT,CGCCGCCC,,Standard,TGTCAGCT,CGCCGCCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037072,,9606,S4360,standard,,from:450 to:450,EGAN00002491048,Normal,Homo sapiens,0,,,PD41305k_163,4396711,,6133STDY8786692,PD41305k_163,,PD41305k_163,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,23, +27037084,EGAN00002490985,,CTCTCCGG,TGCCGGCA,,Standard,CTCTCCGG,TGCCGGCA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037084,,9606,S4360,standard,,from:450 to:450,EGAN00002490985,Normal,Homo sapiens,0,,,PD41305k_164,4396712,,6133STDY8786693,PD41305k_164,,PD41305k_164,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,24, +27037134,EGAN00002490989,,AGAGTTAC,GATGGCTA,,Standard,AGAGTTAC,GATGGCTA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037134,,9606,S4360,standard,,from:450 to:450,EGAN00002490989,Normal,Homo sapiens,0,,,PD41305k_168,4396716,,6133STDY8786697,PD41305k_168,,PD41305k_168,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,25, +27037061,EGAN00002490991,,CTCTTTAT,AAGCTCCG,,Standard,CTCTTTAT,AAGCTCCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037061,,9606,S4360,standard,,from:450 to:450,EGAN00002490991,Normal,Homo sapiens,0,,,PD41305k_170,4396718,,6133STDY8786699,PD41305k_170,,PD41305k_170,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,26, +27037073,EGAN00002490992,,AGAGAGCC,ATAGGCAA,,Standard,AGAGAGCC,ATAGGCAA,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037073,,9606,S4360,standard,,from:450 to:450,EGAN00002490992,Normal,Homo sapiens,0,,,PD41305k_171,4396719,,6133STDY8786700,PD41305k_171,,PD41305k_171,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,27, +27037085,EGAN00002490993,,CATCCACT,CCGGTGCC,,Standard,CATCCACT,CCGGTGCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037085,,9606,S4360,standard,,from:450 to:450,EGAN00002490993,Normal,Homo sapiens,0,,,PD41305k_172,4396720,,6133STDY8786701,PD41305k_172,,PD41305k_172,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,28, +27037086,EGAN00002491001,,CATTCTTC,TAACCGCG,,Standard,CATTCTTC,TAACCGCG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037086,,9606,S4360,standard,,from:450 to:450,EGAN00002491001,Normal,Homo sapiens,0,,,PD41305k_180,4396728,,6133STDY8786709,PD41305k_180,,PD41305k_180,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,29, +27037098,EGAN00002491002,,CTCGACGT,GAAGAGCC,,Standard,CTCGACGT,GAAGAGCC,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037098,,9606,S4360,standard,,from:450 to:450,EGAN00002491002,Normal,Homo sapiens,0,,,PD41305k_181,4396729,,6133STDY8786710,PD41305k_181,,PD41305k_181,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,30, +27037110,EGAN00002491003,,AGTTGCAA,ATCCTGAG,,Standard,AGTTGCAA,ATCCTGAG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037110,,9606,S4360,standard,,from:450 to:450,EGAN00002491003,Normal,Homo sapiens,0,,,PD41305k_182,4396730,,6133STDY8786711,PD41305k_182,,PD41305k_182,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,31, +27037051,EGAN00002491009,,GTAAGATG,AAAGGCTG,,Standard,GTAAGATG,AAAGGCTG,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk user4@sanger.ac.uk,user4@sanger.ac.uk,user1@sanger.ac.uk user2@sanger.ac.uk user3@sanger.ac.uk,user1@sanger.ac.uk,,0,0,30355804,3,27037051,,9606,S4360,standard,,from:450 to:450,EGAN00002491009,Normal,Homo sapiens,0,,,PD41305k_185,4396733,,6133STDY8786714,PD41305k_185,,PD41305k_185,,,1,0,0,Sequencing of blood stem cell-derived colonies.,6133,ImmunoAgeing_Colonies_WGS,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,ImmunoAgeing_Colonies_WGS,32, diff --git a/t/data/samplesheet/novaseq_multirun.csv b/t/data/samplesheet/novaseq_multirun.csv index 4085771d..e4dcfb64 100644 --- a/t/data/samplesheet/novaseq_multirun.csv +++ b/t/data/samplesheet/novaseq_multirun.csv @@ -1,10 +1,10 @@ -[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, -Lane,Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,id_run,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, -1,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863688,0,22802061,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, -2,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863689,0,22802061,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, -3,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863690,0,22802061,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, -4,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863691,0,22802061,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, -1,23356155,7617423,,,HiSeqX PCR free,GGCTTAAG,TCGTGACC,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222813,0,23356155,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7617423,3836420,,7617423,,,3426258,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, -2,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222814,0,22802061,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, -3,23455444,7616265,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222815,0,23455444,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7616265,3835262,,7616265,,,2612688,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, -4,23454971,7615018,,,HiSeqX PCR free,GACCTGAA,TTGGTGAG,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222816,0,23454971,,9606,T4600,,,standard,1,,from:450 to:450,,,Homo sapiens,0,,,7615018,3834015,,7615018,,,2361066,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,id_run,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,purpose,qc_state,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863688,0,22802061,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, +2,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863689,0,22802061,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, +3,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863690,0,22802061,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, +4,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,26480,0,0,22863691,0,22802061,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,9, +1,23356155,7617423,,,HiSeqX PCR free,GGCTTAAG,TCGTGACC,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222813,0,23356155,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7617423,3836420,,7617423,,,3426258,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, +2,22802061,7592352,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222814,0,22802061,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7592352,3811339,,7592352,,,3547031,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, +3,23455444,7616265,,,HiSeqX PCR free,AGTTCAGG,CCAACAGA,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222815,0,23455444,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7616265,3835262,,7616265,,,2612688,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, +4,23454971,7615018,,,HiSeqX PCR free,GACCTGAA,TTGGTGAG,aaaa@sanger.ac.uk,,aaaa@sanger.ac.uk,aaaa@sanger.ac.uk,,28780,0,0,25222816,0,23454971,,9606,T4600,standard,1,from:450 to:450,,,Homo sapiens,0,,,7615018,3834015,,7615018,,,2361066,888,,1,0,0,UK Whole Genome sequencing study,5392,UK Study,Homo_sapiens (GRCh38_15_plus_hs38d1) %5Bminimap2%5D,0,UK Study,4, From 8e9048ed5155a974e18da1e421d252711b301c1f Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 26 Oct 2023 14:05:07 +0100 Subject: [PATCH 15/35] Restricted automatically meargeable to NovaSeq. In practice we never automatically merged rapid runs, this flag was reverted to false for them by the pipeline. Instruments on which rapid runs were performed are no longer in use. --- lib/npg_tracking/illumina/run/long_info.pm | 9 +++------ t/60-illumina-run-long_info.t | 2 +- 2 files changed, 4 insertions(+), 7 deletions(-) diff --git a/lib/npg_tracking/illumina/run/long_info.pm b/lib/npg_tracking/illumina/run/long_info.pm index abe2e2ab..5e321dd4 100644 --- a/lib/npg_tracking/illumina/run/long_info.pm +++ b/lib/npg_tracking/illumina/run/long_info.pm @@ -654,17 +654,14 @@ sub _build_sbs_consumable_version { =head2 all_lanes_mergeable -Returns true if either the NovaSeq Standard (ie not NovaSeqXp) workflow -was used or this was a rapid run since in the latter case same library is used -on both lanes. +Returns true if the NovaSeq Standard (ie not NovaSeqXp) workflow was used +since it is guaranteed that the same library is used on all lanes. =cut sub all_lanes_mergeable { my $self = shift; - return ( - ($self->workflow_type() =~ /NovaSeqStandard/xms) or $self->is_rapid_run() - ); + return ($self->workflow_type() =~ /NovaSeqStandard/xms); } =head2 is_rapid_run diff --git a/t/60-illumina-run-long_info.t b/t/60-illumina-run-long_info.t index ab44defe..7fb47756 100644 --- a/t/60-illumina-run-long_info.t +++ b/t/60-illumina-run-long_info.t @@ -88,7 +88,7 @@ subtest 'retrieving information from runParameters.xml' => sub { if ($f =~ /\.rr\./) { ok ($li->is_rapid_run(), 'is rapid run'); - ok ($li->all_lanes_mergeable(), 'all lanes meargeable'); + ok (!$li->all_lanes_mergeable(), 'lanes are not meargeable'); if ($f =~ /\.truseq\./) { ok (!$li->is_rapid_run_v2(), 'rapid run version is not 2'); ok ($li->is_rapid_run_v1(), 'rapid run version is 1'); From b3525ab0e49e933bfc0e5f1b368cbe7c56cad792 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 26 Oct 2023 18:21:14 +0100 Subject: [PATCH 16/35] Fixed typos --- t/60-illumina-run-long_info.t | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/t/60-illumina-run-long_info.t b/t/60-illumina-run-long_info.t index 7fb47756..5015437a 100644 --- a/t/60-illumina-run-long_info.t +++ b/t/60-illumina-run-long_info.t @@ -88,7 +88,7 @@ subtest 'retrieving information from runParameters.xml' => sub { if ($f =~ /\.rr\./) { ok ($li->is_rapid_run(), 'is rapid run'); - ok (!$li->all_lanes_mergeable(), 'lanes are not meargeable'); + ok (!$li->all_lanes_mergeable(), 'lanes are not mergeable'); if ($f =~ /\.truseq\./) { ok (!$li->is_rapid_run_v2(), 'rapid run version is not 2'); ok ($li->is_rapid_run_v1(), 'rapid run version is 1'); @@ -101,10 +101,10 @@ subtest 'retrieving information from runParameters.xml' => sub { ok (!$li->is_rapid_run(), 'is not rapid run'); if ($f =~ /\.novaseq\./) { if ($f =~ /\.xp\./) { - ok (!$li->all_lanes_mergeable(), 'lanes are not meargeable'); + ok (!$li->all_lanes_mergeable(), 'lanes are not mergeable'); is ($li->workflow_type, 'NovaSeqXp', 'Xp workflow type'); } else { - ok ($li->all_lanes_mergeable(), 'all lanes meargeable'); + ok ($li->all_lanes_mergeable(), 'all lanes mergeable'); is ($li->workflow_type, 'NovaSeqStandard', 'Standard workflow type'); } } From 385d7a5dd5a45e74c91c296fd4df9094c312a215 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 19 Oct 2023 13:21:50 +0100 Subject: [PATCH 17/35] Deleted the code for inline indexes. This was used for Tradis runs when no LIMS support was available. Was not needed for the last 7 years. --- lib/st/api/lims.pm | 84 ---------------------------------------------- 1 file changed, 84 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index c72217f0..fdd2afca 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -316,90 +316,6 @@ for my $m ( @METHODS ){ # All methods are created, now aliases for methods can be defined. alias primer_panel => 'gbs_plex_name'; -=head2 inline_index_read - -index read - -=cut - -has 'inline_index_read' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); - -sub _build_inline_index_read { - my $self = shift; - my @x = _parse_sample_description($self->_sample_description); - return $x[3]; ## no critic (ProhibitMagicNumbers) -} - -has 'inline_index_end' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); - -=head2 inline_index_end - -index end - -=cut - -sub _build_inline_index_end { - my $self = shift; - my @x = _parse_sample_description($self->_sample_description); - return $x[2]; -} - -=head2 inline_index_start - -index start - -=cut - -has 'inline_index_start' => (isa => 'Maybe[Int]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); - -sub _build_inline_index_start { - my $self = shift; - my @x = _parse_sample_description($self->_sample_description); - return $x[1]; -} - -=head2 inline_index_exists - -=cut - -has 'inline_index_exists' => (isa => 'Bool', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); - -sub _build_inline_index_exists { - my $self = shift; - return _tag_sequence_from_sample_description($self->_sample_description) ? 1 : 0; -} - -has '_sample_description' => (isa => 'Maybe[Str]', - is => 'ro', - init_arg => undef, - lazy_build => 1, - ); - -sub _build__sample_description { - my $self = shift; - return $self->sample_description if ($self->sample_description); - foreach my $c ($self->children) { - return $c->sample_description if ($c->sample_description); - } - return; -} - =head2 is_phix_spike True for a plex library that is the spiked phiX. From fd3a5feb373fe73550f55d7f186ee77a374f1cfb Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Thu, 19 Oct 2023 14:16:35 +0100 Subject: [PATCH 18/35] Dropped derived library type and barcode sequence. --- lib/st/api/lims.pm | 84 +++++++++++----------------------------------- t/40-st-lims.t | 4 ++- 2 files changed, 22 insertions(+), 66 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index fdd2afca..85ca65c4 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -203,6 +203,7 @@ sub BUILD { Readonly::Hash my %ATTRIBUTE_LIST_METHODS => { 'library' => [qw/ id name + type /], 'sample' => [qw/ accession_number cohort @@ -357,9 +358,6 @@ sub _build_tag_sequence { Read-only array accessor, not possible to set from the constructor. Empty array on a lane level and for zero tag_index. -Might return not the index given by LIMs, but the one contained in the -sample description. - If dual index is used, the array contains two sequences. The secons index might come from LIMS or, if LIMs has one long index, it will be split in two. @@ -372,34 +370,24 @@ has 'tag_sequences' => (isa => 'ArrayRef', sub _build_tag_sequences { my $self = shift; - my ($seq, $seq2); + my @sqs = (); + if ($self->tag_index) { - if (!$self->spiked_phix_tag_index || $self->tag_index != $self->spiked_phix_tag_index) { - if ($self->sample_description) { - $seq = _tag_sequence_from_sample_description($self->sample_description); + my $seq = $self->default_tag_sequence; + if ($seq) { + push @sqs, $seq; + $seq = $self->default_tagtwo_sequence; + if ($seq) { + push @sqs, $seq; } } - if (!$seq) { - $seq = $self->default_tag_sequence; - if ($seq && $self->default_tagtwo_sequence) { - $seq2 = $self->default_tagtwo_sequence; - } - } - } - my @sqs = (); - if ($seq) { - push @sqs, $seq; - } - if ($seq2) { - push @sqs, $seq2; - } - - if (scalar @sqs == 1) { - if (length($sqs[0]) == $DUAL_INDEX_TAG_LENGTH) { - my $tag_length = $DUAL_INDEX_TAG_LENGTH/2; - push @sqs, substr $sqs[0], $tag_length; - $sqs[0] = substr $sqs[0], 0, $tag_length; + if (scalar @sqs == 1) { + if (length($sqs[0]) == $DUAL_INDEX_TAG_LENGTH) { + my $tag_length = $DUAL_INDEX_TAG_LENGTH/2; + push @sqs, substr $sqs[0], $tag_length; + $sqs[0] = substr $sqs[0], 0, $tag_length; + } } } @@ -1101,44 +1089,14 @@ has 'library_type' => (isa => 'Maybe[Str]', ); sub _build_library_type { my $self = shift; - if($self->is_pool) { return; } - return _derived_library_type($self); -} -sub _derived_library_type { - my $o = shift; - my $type = $o->default_library_type; - if ($o->tag_index && $o->sample_description && - _tag_sequence_from_sample_description($o->sample_description)) { - $type = '3 prime poly-A pulldown'; + my $type; + if (!$self->is_pool) { + $type = $self->default_library_type; } $type ||= undef; - return $type; -} - -sub _tag_sequence_from_sample_description { - my $desc = shift; - my @x = _parse_sample_description($desc); - return $x[0]; -} -sub _parse_sample_description { - my $desc = shift; - my $tag=undef; - my $start=undef; - my $end=undef; - my $read=undef; - if ($desc && (($desc =~ m/base\ indexing\ sequence/ismx) && ($desc =~ m/enriched\ mRNA/ismx))) { - ($tag) = $desc =~ /\(([ACGT]+)\)/smx; - if ($desc =~ /bases\ (\d+)\ to\ (\d+)\ of\ read\ 1/smx) { - ($start, $end, $read) = ($1, $2, 1); - } elsif ($desc =~ /bases\ (\d+)\ to\ (\d+)\ of\ non\-index\ read\ (\d)/smx) { - ($start, $end, $read) = ($1, $2, $3); - } else { - croak q[Error parsing sample description ] . $desc; - } - } - return ($tag, $start, $end, $read); + return $type; } =head2 library_types @@ -1146,10 +1104,6 @@ sub _parse_sample_description { A list of library types, excluding spiked phix library =cut -sub library_types { - my ($self) = @_; - return $self->_list_of_attributes('_derived_library_type',0); -} =head2 driver_method_list diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 7d23e601..8c6a59d3 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -861,7 +861,7 @@ subtest 'Consent and separation of human data' => sub { }; subtest 'Library types' => sub { - plan tests => 6; + plan tests => 7; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/4pool4libs_extended.csv'; @@ -872,6 +872,8 @@ subtest 'Library types' => sub { is($lims->library_type, 'No PCR', 'library type'); $lims = st::api::lims->new(id_run => 9999, position => 8); is($lims->library_type, undef, 'library type undefined for a pool'); + is(join(q[,], $lims->library_types), q[Pre-quality controlled], + 'library types'); $lims = st::api::lims->new(id_run => 9999, position => 8, tag_index => 0); is($lims->library_type, undef, 'library type undefined for tag 0'); $lims = st::api::lims->new(id_run => 9999, position => 8, tag_index => 88); From a246c4441f2ca9095de29c11cc04cbace2929ed9 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 27 Oct 2023 17:55:13 +0100 Subject: [PATCH 19/35] Move docs about plural methods closer to the code --- lib/st/api/lims.pm | 158 ++++++++++++++++++--------------------------- 1 file changed, 62 insertions(+), 96 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 85ca65c4..0e1496e3 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -221,6 +221,68 @@ Readonly::Hash my %ATTRIBUTE_LIST_METHODS => { /] }; +=head2 library_names + +A list of library names. if $self->is_pool is true, returns unique library +names of plex-level objects, otherwise returns object's own library name. +Takes an optional argument with_spiked_control, wich defaults to true. + +=head2 library_ids + +Similar to library_names, but for ids. + +=head2 library_types + +Similar to library_names, but for types. + +=head2 sample_names + +A list of sample names. if $self->is_pool is true, returns unique sample +names of plex-level objects, otherwise returns object's own sample name. +Takes an optional argument with_spiked_control, wich defaults to true. + +=head2 sample_cohorts + +Similar to sample_names, but for cohorts. + +=head2 sample_donor_ids + +Similar to sample_names, but for donor_ids. + +=head2 sample_ids + +Similar to sample_names, but for ids. + +=head2 sample_public_names + +Similar to sample_names, but for public_names. + +=head2 sample_supplier_names + +Similar to sample_names, but for supplier_names. + +=head2 study_names + +A list of study names. if $self->is_pool is true, returns unique study +names of plex-level objects, otherwise returns object's own study name. +Takes an optional argument with_spiked_control, wich defaults to true. + +=head2 study_accession_numbers + +Similar to study_names, but for accession_numbers. + +=head2 study_ids + +Similar to study_names, but for ids. + +=head2 study_titles + +Similar to study_names, but for study_titles. + +=cut + +# Dynamicaly generate methods for getting 'plural' values. +# The methods are documented above. foreach my $object_type (keys %ATTRIBUTE_LIST_METHODS) { foreach my $property (@{$ATTRIBUTE_LIST_METHODS{$object_type}}) { my $attr_name = join q[_], $object_type, $property; @@ -987,96 +1049,6 @@ sub _single_attribute { return; } -=head2 library_names - -A list of library names. if $self->is_pool is true, returns unique library -names of plex-level objects, otherwise returns object's own library name. -Takes an optional argument with_spiked_control, wich defaults to true. - - -=cut - -=head2 library_ids - -Similar to library_names, but for ids. - -=cut - - -=head2 sample_names - -A list of sample names. if $self->is_pool is true, returns unique sample -names of plex-level objects, otherwise returns object's own sample name. -Takes an optional argument with_spiked_control, wich defaults to true. - -=cut - - -=head2 sample_cohorts - -Similar to sample_names, but for cohorts. - -=cut - - -=head2 sample_donor_ids - -Similar to sample_names, but for donor_ids. - -=cut - - -=head2 sample_ids - -Similar to sample_names, but for ids. - -=cut - - -=head2 sample_public_names - -Similar to sample_names, but for public_names. - -=cut - - -=head2 sample_supplier_names - -Similar to sample_names, but for supplier_names. - -=cut - - -=head2 study_names - -A list of study names. if $self->is_pool is true, returns unique study -names of plex-level objects, otherwise returns object's own study name. -Takes an optional argument with_spiked_control, wich defaults to true. - -=cut - - -=head2 study_accession_numbers - -Similar to study_names, but for accession_numbers. - -=cut - - -=head2 study_ids - -Similar to study_names, but for ids. - -=cut - - -=head2 study_titles - -Similar to study_names, but for study_titles. - -=cut - - =head2 library_type Read-only accessor, not possible to set from the constructor. @@ -1099,12 +1071,6 @@ sub _build_library_type { return $type; } -=head2 library_types - -A list of library types, excluding spiked phix library - -=cut - =head2 driver_method_list A sorted list of methods that should be implemented by a driver From 6f077e72436f1d6046bc1136e9c2825615d51dd4 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 30 Oct 2023 09:47:47 +0000 Subject: [PATCH 20/35] Limit DRAGEN analysis to human samples only. --- lib/npg/samplesheet/novaseq_xseries.pm | 10 ++-------- 1 file changed, 2 insertions(+), 8 deletions(-) diff --git a/lib/npg/samplesheet/novaseq_xseries.pm b/lib/npg/samplesheet/novaseq_xseries.pm index bbdabd79..da770215 100755 --- a/lib/npg/samplesheet/novaseq_xseries.pm +++ b/lib/npg/samplesheet/novaseq_xseries.pm @@ -33,16 +33,10 @@ Readonly::Array my @RNA_ANALYSES_REFS => qw(tophat2 star hisat2); Readonly::Array my @RNA_ANALYSES_LIB_TYPES => qw(rna cdna); Readonly::Array my @TENX_ANALYSES_LIB_TYPES => qw(chromium haplotagging); Readonly::Array my @VAR_CALL_MODES => - qw(None SmallVariantCaller AllVariantCallers); + qw(None SmallVariantCaller AllVariantCallers); -# Not mapping PhiX on purpose - an easy way to avoid invoking -# an extra Germline pipeline in a situation when the number of -# unique analysis configurations is limited to 4 locally and 8 -# in the cloud, with one of them being BCLConvert. -# Was 'PhiX' => 'phix-rna-8-1667499364-2' Readonly::Hash my %REFERENCE_MAPING => ( - 'Homo_sapiens'=> 'hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2', - 'Escherichia_coli' => 'eschColi_K12_1-rna-8-1667494624-2', + 'Homo_sapiens' => 'hg38-alt_masked.cnv.graph.hla.rna-8-1667497097-2' ); # The version of the DRAGEN software currently on-board of the instrument. From 8c37ec4a955b40ffbbb3a40428f3b946b35f2a76 Mon Sep 17 00:00:00 2001 From: mgcam Date: Mon, 30 Oct 2023 19:51:17 +0000 Subject: [PATCH 21/35] =?UTF-8?q?Removed=20fallback=20to=20study=20ref=20g?= =?UTF-8?q?enome=20for=20complex=20tag=20zero=20and=20lane-le=E2=80=A6=20(?= =?UTF-8?q?#761)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Removed fallback to study ref genome for complex tag zero and lane-level objects * Fixed a typo in the name of a variable * Corrected the scope of the variable --- lib/st/api/lims.pm | 23 +++++++++++++++++++- t/40-st-lims.t | 52 ++++++++++++++++++++++++++++++++++++++++------ 2 files changed, 68 insertions(+), 7 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 0e1496e3..89a76ebd 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -212,6 +212,7 @@ Readonly::Hash my %ATTRIBUTE_LIST_METHODS => { id name public_name + reference_genome supplier_name /], 'study' => [qw/ accession_number @@ -522,7 +523,9 @@ sub _build_required_insert_size { Read-only accessor, not possible to set from the constructor. Returns pre-set reference genome, retrieving it either from a sample, -or, failing that, from a study. +or, failing that, from a study. The exception from the latter rule is +tag zero or lane objects, where a fall-back to the study genome is +disabled if the child objects have different sample reference genomes. =cut has 'reference_genome' => (isa => 'Maybe[Str]', @@ -534,6 +537,24 @@ sub _build_reference_genome { my $self = shift; my $rg = $self->_trim_value($self->sample_reference_genome); if (!$rg ) { + if ($self->is_pool || $self->is_composition) { + my @children = $self->children(); + if ($self->is_composition) { + # Tag zero and lane components have their own children. + my @tmp_children = map { ($_->children) } @children; + if (@tmp_children) { + @children = @tmp_children; + } + } + my @sample_ref_genomes = + grep { $_ } + map { $self->_trim_value($_->sample_reference_genome) } + grep { !$_->is_phix_spike } + @children; + if (@sample_ref_genomes) { + return; + } + } $rg = $self->_trim_value($self->study_reference_genome); } return $rg; diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 8c6a59d3..e9bd09d9 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -665,7 +665,7 @@ subtest 'Insert size' => sub { }; subtest 'Study and sample properties' => sub { - plan tests => 47; + plan tests => 75; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/4pool4libs_extended.csv'; @@ -728,22 +728,24 @@ subtest 'Study and sample properties' => sub { my $ref = 'Homo_sapiens (GRCh38_15_plus_hs38d1) [minimap2]'; for my $l ( st::api::lims->new(id_run => 47539, position => 1), - st::api::lims->new(id_run => 47537, position => 1, tag_index => 0) + st::api::lims->new(id_run => 47537, position => 1, tag_index => 0), + st::api::lims->new(rpt_list => '47539:1'), + st::api::lims->new(rpt_list => '47539:1:0') ) { is( $l->study_name(), $study_name, 'study name'); is( $l->sample_name, undef, 'sample name undefined'); is( $l->sample_reference_genome, undef, 'sample reference genome undefined'); is( $l->study_reference_genome, $ref, 'study reference genome'); - is( $l->reference_genome, $ref, 'reference genome - fallback to study'); + is( $l->reference_genome, undef, 'no fallback to study'); } - my $sample_ref = 'Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla)'; + my $ref2 = 'Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla)'; $lims = st::api::lims->new(id_run => 47537, position => 1, tag_index => 1); is( $lims->study_name(), $study_name, 'study name'); is( $lims->sample_name, 'RefStds_PCR8021331', 'sample name'); - is( $lims->sample_reference_genome, $sample_ref, 'sample reference genome'); + is( $lims->sample_reference_genome, $ref2, 'sample reference genome'); is( $lims->study_reference_genome, $ref, 'study reference genome'); - is( $lims->reference_genome, $sample_ref, 'reference genome as for the sample'); + is( $lims->reference_genome, $ref2, 'reference genome as for the sample'); $lims = st::api::lims->new(id_run => 47537, position => 4, tag_index => 2); is( $lims->study_name(),$study_name, 'study name'); @@ -751,6 +753,44 @@ subtest 'Study and sample properties' => sub { is( $lims->sample_reference_genome, undef, 'sample reference genome undefined'); is( $lims->study_reference_genome, $ref, 'study reference genome'); is( $lims->reference_genome, $ref, 'reference genome - fall back to study'); + + $lims = st::api::lims->new(id_run => 47537, position => 4, tag_index => 1); + is( $lims->sample_reference_genome, $ref2, 'sample reference genome'); + is( $lims->study_reference_genome, $ref, 'study reference genome'); + is( $lims->reference_genome, $ref2, 'reference genome'); + + # The fact that in tests below sample_reference_genome and, as a consequence, + # reference_genome methods return a reference rather than stay undefined + # seems wrong. The two samples in the pool have the same referenceand and + # for one it is undefined. If in this case no value was considered as an + # unknown reference, both methods would have returned an undefined value. + for my $l ( + st::api::lims->new(id_run => 47539, position => 4), + st::api::lims->new(id_run => 47537, position => 4, tag_index => 0), + ) { + is( $l->sample_reference_genome, $ref2, 'sample reference genome'); + is( $l->study_reference_genome, $ref, 'study reference genome'); + is( $l->reference_genome, $ref2, 'ref genome'); + } + + $lims = st::api::lims->new(rpt_list => '47539:1:0;47539:4:0'); + is( $lims->sample_reference_genome, undef, 'sample reference genome undefined'); + is( $lims->study_reference_genome, $ref, 'study reference genome'); + is( $lims->reference_genome, undef, 'ref genome'); + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/samplesheet_27483.csv'; + # Spiked lane, no sample references, single study. + $ref = 'Homo_sapiens (GRCh38_15 + ensembl_78_transcriptome)'; + for my $l ( + st::api::lims->new(id_run => 27483, position => 8), + st::api::lims->new(id_run => 27483, position => 8, tag_index => 0), + ) { + is( $l->sample_reference_genome, undef, 'sample reference genome undefined'); + is( $l->study_reference_genome, $ref, 'study reference genome'); + is( $l->reference_genome, $ref, 'fall back to study genome'); + } + }; subtest 'Bait name' => sub { From ad5bbf0cadd8aaafe6b1d1cb0b3270ad1e7659f0 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 31 Oct 2023 10:05:46 +0000 Subject: [PATCH 22/35] Record all recent changes --- Changes | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/Changes b/Changes index be449358..f3ef1b9e 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,35 @@ LIST OF CHANGES + - Removed the use of 'xml' lims driver from all tests. + - Deleted 'xml' lims driver class and all classes, which supported this + functionality, together with all related tests and test data. + - In release 97.0.0, ihe default LIMS driver type in samplesheet generation + was changed to 'ml_warehouse'. Following this change, the code for + auto-generation of MiSeq default samplesheets is now simplified to exclude + an explicit creation of LIMS objects. + - Changes to st::api::lims, which are not related to the 'xml' lims driver + removal: + - deleted all previously deprecated methods ('seq_qc_state', + 'associated_lims', 'associated_child_lims', 'associated_child_lims_ia'); + - deleted methods, for which we do not have data in ml warehouse, our + primary source of LIMS data ('request_id', 'project_id', 'project_name'); + - deleted all code for computing inline tag indexes and inferring + tag sequences and library types from sample description since + definitions like this have not been in use for the last six years; + - reimplemented the 'reference_genome' method to exclude a fallback to + a study reference for tag zero and lane-level objects when samples + have different references. + - Restricted the 'all_lanes_mergeable' flag in the 'lonf_info' role to + NovaSeq Standard workflow, ie dropped an additional case of HiSeq Rapid Run + since HiSeq instruments are no longer used. + - Updated DBIx classes from the prod database. Changes are due to the MySQL + database server upgrade to v8.+ + - Finding the runfolder path - stopped errors being raised when a runfolder + is found in 'analysis' or 'outgoing' in the presence of a duplicate runfolder + in 'incoming' (the duplicates in 'incoming' are sometimes created by + instruments well after the run was mirrored and the runfolder moved to + 'analysis'). The duplicate runfolder in 'incoming' is disregarded'. + release 97.0.0 - Change CI workflow to standard file name - Change to Perl versions from Perlbrew From 10352367d73b68154838e17f2579858ed9148a41 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 31 Oct 2023 18:01:21 +0000 Subject: [PATCH 23/35] Fixed typos and deleted superfluous commas --- Changes | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/Changes b/Changes index f3ef1b9e..8f538bfc 100644 --- a/Changes +++ b/Changes @@ -1,9 +1,9 @@ LIST OF CHANGES - Removed the use of 'xml' lims driver from all tests. - - Deleted 'xml' lims driver class and all classes, which supported this + - Deleted 'xml' lims driver class and all classes which supported this functionality, together with all related tests and test data. - - In release 97.0.0, ihe default LIMS driver type in samplesheet generation + - In release 97.0.0, the default LIMS driver type in samplesheet generation was changed to 'ml_warehouse'. Following this change, the code for auto-generation of MiSeq default samplesheets is now simplified to exclude an explicit creation of LIMS objects. @@ -11,7 +11,7 @@ LIST OF CHANGES removal: - deleted all previously deprecated methods ('seq_qc_state', 'associated_lims', 'associated_child_lims', 'associated_child_lims_ia'); - - deleted methods, for which we do not have data in ml warehouse, our + - deleted methods for which we do not have data in ml warehouse, our primary source of LIMS data ('request_id', 'project_id', 'project_name'); - deleted all code for computing inline tag indexes and inferring tag sequences and library types from sample description since @@ -19,7 +19,7 @@ LIST OF CHANGES - reimplemented the 'reference_genome' method to exclude a fallback to a study reference for tag zero and lane-level objects when samples have different references. - - Restricted the 'all_lanes_mergeable' flag in the 'lonf_info' role to + - Restricted the 'all_lanes_mergeable' flag in the 'long_info' role to NovaSeq Standard workflow, ie dropped an additional case of HiSeq Rapid Run since HiSeq instruments are no longer used. - Updated DBIx classes from the prod database. Changes are due to the MySQL From c9a37bda13ad549af647674f718caa03668c1bea Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 27 Oct 2023 16:41:29 +0100 Subject: [PATCH 24/35] Added a method for aggregation by library --- lib/st/api/lims.pm | 80 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 80 insertions(+) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 89a76ebd..1b3fa7bd 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -910,6 +910,86 @@ sub aggregate_xlanes { return @aggregated; } +=head2 aggregate_libraries + +=cut +sub aggregate_libraries() { + my ($self, $lane_lims_array) = @_; + + my @id_runs = uniq map { $_->id_run } @{$lane_lims_array}; + if (@id_runs != 1) { + croak 'Multiple run IDs in a potential library merge'; + } + + my $all_lims_objects = {}; + my $lims_objects_by_library = {}; + + my @all_single_lims_objs = map { $_->is_pool ? $_->children() : $_ } + @{$lane_lims_array}; + + foreach my $obj (@all_single_lims_objs) { + if ($obj->is_control()) { # Do not merge spiked PhiX libraries. + push @{$all_lims_objects->{'single'}}, $obj; + } else { + push @{$lims_objects_by_library->{$obj->library_id}}, $obj; + } + } + + my $merge_set = {}; + + # Do not use $self for this to retain ability to use this method as a class + # method. + my %init = %{$lane_lims_array->[0]->_driver_arguments()}; + + foreach my $library_id (keys %{$lims_objects_by_library}) { + my @lib_lims = @{$lims_objects_by_library->{$library_id}}; + if (@lib_lims == 1) { + push @{$all_lims_objects->{'single'}}, $lib_lims[0]; + } else { + my @study_ids = uniq map { $_->study_id } @lib_lims; + if (@study_ids != 1) { + croak 'Multiple studies in a potential merge'; + } + my @tag_indexes = + uniq + map { defined $_->tag_index ? $_->tag_index : 'undefined' } + @lib_lims; + if (@tag_indexes != 1) { + croak 'Inconsistent tag indexes in a potential merge'; + } + my @lanes = uniq map {$_->position} @lib_lims; + if (@lanes != @lib_lims) { + croak 'Intra-lane merge is detected in a potential merge'; + } + my $lane_set = join q[,], @lanes; + $all_lims_objects->{'merges'}->{$lane_set}->{$tag_indexes[0]} = + __PACKAGE__->new( + %init, + rpt_list => npg_tracking::glossary::rpt->deflate_rpts(\@lib_lims) + ); + } + } + + # Lane sets should not intersect. + my @positions = + map { (split /,/smx, $_) } + keys %{$all_lims_objects->{'merges'}}; + if (@positions != uniq @positions) { + croak 'No clean split between lanes in potential merges'; + } + + # Within each set sort LIMS objects by tag index and keep + # the sorted list. + foreach my $lane_set ( keys %{$all_lims_objects->{'merges'}} ) { + my @sorted_lims_onjects = + map {$all_lims_objects->{'merges'}->{$lane_set}->{$_}} + (sort { $a <=> $b } keys %{$all_lims_objects->{'merges'}->{$lane_set}}); + $all_lims_objects->{'merges'}->{$lane_set} = \@sorted_lims_onjects; + } + + return $all_lims_objects; +} + =head2 create_tag_zero_object Using id_run and position values of this object, creates and returns From 00ba90ef3ab61158b7c11eb429afa25baf65d550 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 14 Nov 2023 12:51:49 +0000 Subject: [PATCH 25/35] Moved some tests to a new test script. Moved tests for aggregation across lanes to a new test scripts. Tests for a new merge by library method will be added to this new test script. --- MANIFEST | 1 + t/40-st-lims-merge.t | 244 +++++++++++++++++++++++++++++++++++++++++++ t/40-st-lims.t | 238 +---------------------------------------- 3 files changed, 246 insertions(+), 237 deletions(-) create mode 100644 t/40-st-lims-merge.t diff --git a/MANIFEST b/MANIFEST index 346e5a4b..b06146ca 100644 --- a/MANIFEST +++ b/MANIFEST @@ -395,6 +395,7 @@ t/34-monitor-runfolder-staging.t t/34-monitor-runfolder.t t/34-monitor-staging.t t/35-monitor_one_runfolder.t +t/40-st-lims-merge.t t/40-st-lims-mlwarehouse.t t/40-st-lims-ml_warehouse-drivers.t t/40-st-lims-samplesheet.t diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t new file mode 100644 index 00000000..01bc15e3 --- /dev/null +++ b/t/40-st-lims-merge.t @@ -0,0 +1,244 @@ +use strict; +use warnings; +use Test::More tests => 4; +use Test::Exception; + +use_ok('st::api::lims'); + +subtest 'Aggregation across lanes for pools' => sub { + plan tests => 85; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + + my $l = st::api::lims->new(rpt_list => '25846:1:3'); + throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, + 'method cannot be run for a composition'; + $l = st::api::lims->new(id_run => 25846, position => 1); + throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, + 'method cannot be run for a lane-level object'; + $l = st::api::lims->new(id_run => 25846, position => 1, tag_index => 4); + throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, + 'method cannot be run for a plex-level object'; + + $l = st::api::lims->new(id_run => 25846); + + throws_ok { $l->aggregate_xlanes(qw/2 10/) } + qr/Requested position 10 does not exists in /, + 'error if requested position does not exist'; + + my @merged = $l->aggregate_xlanes(); + is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); + my $tag_zero = pop @merged; + my $tag_spiked = pop @merged; + my $tag_last = pop @merged; + my $tag_first = shift @merged; + is ($tag_zero->rpt_list, '25846:1:0;25846:2:0;25846:3:0;25846:4:0', + 'rpt list for tag zero object'); + is ($tag_spiked->rpt_list, '25846:1:888;25846:2:888;25846:3:888;25846:4:888', + 'rpt list for spiked in tag object'); + is ($tag_last->rpt_list, '25846:1:21;25846:2:21;25846:3:21;25846:4:21', + 'rpt list for tag 21 object'); + is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1', + 'rpt list for tag 1 object'); + + @merged = $l->aggregate_xlanes(qw/1 4/); + is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); + $tag_zero = pop @merged; + $tag_spiked = pop @merged; + $tag_last = pop @merged; + $tag_first = shift @merged; + is ($tag_zero->rpt_list, '25846:1:0;25846:4:0', + 'rpt list for tag zero object'); + is ($tag_spiked->rpt_list, '25846:1:888;25846:4:888', + 'rpt list for spiked in tag object'); + is ($tag_last->rpt_list, '25846:1:21;25846:4:21', + 'rpt list for tag 21 object'); + is ($tag_first->rpt_list, '25846:1:1;25846:4:1', + 'rpt list for tag 1 object'); + + @merged = $l->aggregate_xlanes(qw/1/); + is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); + $tag_zero = pop @merged; + $tag_spiked = pop @merged; + $tag_last = pop @merged; + $tag_first = shift @merged; + is ($tag_zero->rpt_list, '25846:1:0', 'rpt list for tag zero object'); + is ($tag_spiked->rpt_list, '25846:1:888', 'rpt list for spiked in tag object'); + is ($tag_last->rpt_list, '25846:1:21', 'rpt list for tag 21 object'); + is ($tag_first->rpt_list, '25846:1:1', 'rpt list for tag 1 object'); + + @merged = $l->aggregate_xlanes(); + is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); + $tag_zero = pop @merged; + $tag_spiked = pop @merged; + $tag_last = pop @merged; + $tag_first = shift @merged; + is ($tag_zero->rpt_list, '25846:1:0;25846:2:0;25846:3:0;25846:4:0', + 'rpt list for tag zero object'); + is ($tag_spiked->rpt_list, '25846:1:888;25846:2:888;25846:3:888;25846:4:888', + 'rpt list for spiked in tag object'); + is ($tag_last->rpt_list, '25846:1:21;25846:2:21;25846:3:21;25846:4:21', + 'rpt list for tag 21 object'); + is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1', + 'rpt list for tag 1 object'); + + my $expected = { + '25846:1:0;25846:2:0;25846:3:0;25846:4:0' => { + 'sample_id' => undef, + 'sample_name' => undef, + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 5318, + 'study_name' => 'NovaSeq testing', + 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', + 'library_id' => undef, + 'library_name' => undef, + 'library_type' => 'Standard', + 'default_tag_sequence' => undef, + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }, + '25846:1:888;25846:2:888;25846:3:888;25846:4:888' => { + 'sample_id' => '1255141', + 'sample_name' => 'phiX_for_spiked_buffers', + 'sample_common_name' => undef, + 'study_id' => 198, + 'study_name' => 'Illumina Controls', + 'reference_genome' => undef, + 'library_id' => '17883061', + 'library_name' => '17883061', + 'library_type' => undef, + 'default_tag_sequence' => 'ACAACGCAATC', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }, + '25846:1:21;25846:2:21;25846:3:21;25846:4:21' => { + 'sample_id' => '3681772', + 'sample_name' => '5318STDY7462477', + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 5318, + 'study_name' => 'NovaSeq testing', + 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', + 'library_id' => '21059089', + 'library_name' => '21059089', + 'library_type' => 'Standard', + 'default_tag_sequence' => 'TCGAGCGT', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }, + '25846:1:1;25846:2:1;25846:3:1;25846:4:1' => { + 'sample_id' => '3681752', + 'sample_name' => '5318STDY7462457', + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 5318, + 'study_name' => 'NovaSeq testing', + 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', + 'library_id' => '21059039', + 'library_name' => '21059039', + 'library_type' => 'Standard', + 'default_tag_sequence' => 'ATCACGTT', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + } + }; + + for my $o (($tag_zero, $tag_spiked, $tag_first, $tag_last)) { + my $rpt_list = $o->rpt_list; + ok (!defined $o->id_run, "id_run not defined for $rpt_list"); + for my $method ( qw/ + sample_id sample_name sample_common_name + study_id study_name reference_genome + library_id library_name library_type + default_tag_sequence + /) { + is ($o->$method, $expected->{$rpt_list}->{$method}, "$method for $rpt_list"); + } + ok ($o->study_alignments_in_bam, "alignment true for $rpt_list"); + ok (!$o->study_contains_nonconsented_human, "nonconsented_human false for $rpt_list"); + } + + ok ($tag_spiked->is_phix_spike, 'is phix spike'); + ok (!$tag_first->is_phix_spike, 'is not phix spike'); + ok (!$tag_zero->is_phix_spike, 'is not phix spike'); + + is (join(q[:], $tag_zero->study_names), 'Illumina Controls:NovaSeq testing', + 'study names including spiked phix'); + is (join(q[:], $tag_zero->study_names(1)), 'Illumina Controls:NovaSeq testing', + 'sudy names including spiked phix'); + is (join(q[:], $tag_zero->study_names(0)), 'NovaSeq testing', + 'study names excluding spiked phix'); + + my @sample_names = qw/ + 5318STDY7462457 5318STDY7462458 5318STDY7462459 5318STDY7462460 5318STDY7462461 + 5318STDY7462462 5318STDY7462463 5318STDY7462464 5318STDY7462465 5318STDY7462466 + 5318STDY7462467 5318STDY7462468 5318STDY7462469 5318STDY7462470 5318STDY7462471 + 5318STDY7462472 5318STDY7462473 5318STDY7462474 5318STDY7462475 5318STDY7462476 + 5318STDY7462477 /; + + is (join(q[:], $tag_zero->sample_names(0)), join(q[:], @sample_names), + 'sample names excluding spiked phix'); + push @sample_names, 'phiX_for_spiked_buffers'; + is (join(q[:], $tag_zero->sample_names()), join(q[:], @sample_names), + 'sample names including spiked phix'); + is (join(q[:], $tag_zero->sample_names(1)), join(q[:], @sample_names), + 'sample names including spiked phix'); +}; + +subtest 'Aggregation across lanes for non-pools' => sub { + plan tests => 13; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_rapidrun_nopool.csv'; + my @merged = st::api::lims->new(id_run => 22672)->aggregate_xlanes(); + + my $l = $merged[0]; + is (scalar @merged, 1, 'one object returned'); + is ($l->rpt_list, '22672:1;22672:2', 'correct rpt_list'); + ok (!defined $l->id_run, "id_run not defined"); + ok (!$l->is_phix_spike, 'is not phix spike'); + + my $expected = { + 'sample_id' => '2917461', + 'sample_name' => '4600STDY6702635', + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 4600, + 'study_name' => 'Osteosarcoma_WGBS', + 'reference_genome' => 'Not suitable for alignment', + 'library_id' => '18914827', + 'library_name' => '18914827', + 'library_type' => 'Bisulphite pre quality controlled', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }; + + for my $method ( qw/ + sample_id sample_name sample_common_name + study_id study_name reference_genome + library_id library_name library_type + /) { + is ($l->$method, $expected->{$method}, "$method"); + } +}; + +subtest 'Aggregation across lanes for a tag' => sub { + plan tests => 13; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + + my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1'); + + my $e = qr/id_run and position are expected as arguments/; + throws_ok { $l->create_lane_object() } $e, 'no arguments - error'; + throws_ok { $l->create_lane_object(1) } $e, 'one argument - error'; + throws_ok { $l->create_lane_object(1, 0) } $e, + 'one of argument is false - error'; + + for my $p ((1,2)) { + my $lane_l = $l->create_lane_object(25846, $p); + is ($lane_l->id_run, 25846, 'run id is 25846'); + is ($lane_l->position, $p, "position is $p"); + is ($lane_l->rpt_list, undef, 'rpt_list is undefined'); + is ($lane_l->tag_index, undef, 'tag index is undefined'); + ok ($lane_l->is_pool, 'the entity is a pool'); + } +}; + +1; diff --git a/t/40-st-lims.t b/t/40-st-lims.t index e9bd09d9..37dba533 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -1,6 +1,6 @@ use strict; use warnings; -use Test::More tests => 19; +use Test::More tests => 16; use Test::Exception; use Test::Warn; use File::Temp qw/ tempdir /; @@ -343,242 +343,6 @@ subtest 'Samplesheet driver for arbitrary compositions' => sub { is ($ss->tag_index, 4, 'correct tag_index'); }; -subtest 'Aggregation across lanes for pools' => sub { - plan tests => 85; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; - - my $l = st::api::lims->new(rpt_list => '25846:1:3'); - throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, - 'method cannot be run for a composition'; - $l = st::api::lims->new(id_run => 25846, position => 1); - throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, - 'method cannot be run for a lane-level object'; - $l = st::api::lims->new(id_run => 25846, position => 1, tag_index => 4); - throws_ok { $l->aggregate_xlanes() } qr/Not run-level object/, - 'method cannot be run for a plex-level object'; - - $l = st::api::lims->new(id_run => 25846); - - throws_ok { $l->aggregate_xlanes(qw/2 10/) } - qr/Requested position 10 does not exists in /, - 'error if requested position does not exist'; - - my @merged = $l->aggregate_xlanes(); - is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); - my $tag_zero = pop @merged; - my $tag_spiked = pop @merged; - my $tag_last = pop @merged; - my $tag_first = shift @merged; - is ($tag_zero->rpt_list, '25846:1:0;25846:2:0;25846:3:0;25846:4:0', - 'rpt list for tag zero object'); - is ($tag_spiked->rpt_list, '25846:1:888;25846:2:888;25846:3:888;25846:4:888', - 'rpt list for spiked in tag object'); - is ($tag_last->rpt_list, '25846:1:21;25846:2:21;25846:3:21;25846:4:21', - 'rpt list for tag 21 object'); - is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1', - 'rpt list for tag 1 object'); - - @merged = $l->aggregate_xlanes(qw/1 4/); - is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); - $tag_zero = pop @merged; - $tag_spiked = pop @merged; - $tag_last = pop @merged; - $tag_first = shift @merged; - is ($tag_zero->rpt_list, '25846:1:0;25846:4:0', - 'rpt list for tag zero object'); - is ($tag_spiked->rpt_list, '25846:1:888;25846:4:888', - 'rpt list for spiked in tag object'); - is ($tag_last->rpt_list, '25846:1:21;25846:4:21', - 'rpt list for tag 21 object'); - is ($tag_first->rpt_list, '25846:1:1;25846:4:1', - 'rpt list for tag 1 object'); - - @merged = $l->aggregate_xlanes(qw/1/); - is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); - $tag_zero = pop @merged; - $tag_spiked = pop @merged; - $tag_last = pop @merged; - $tag_first = shift @merged; - is ($tag_zero->rpt_list, '25846:1:0', 'rpt list for tag zero object'); - is ($tag_spiked->rpt_list, '25846:1:888', 'rpt list for spiked in tag object'); - is ($tag_last->rpt_list, '25846:1:21', 'rpt list for tag 21 object'); - is ($tag_first->rpt_list, '25846:1:1', 'rpt list for tag 1 object'); - - @merged = $l->aggregate_xlanes(); - is (scalar @merged, 23, 'number of aggregates is number of tags plus two'); - $tag_zero = pop @merged; - $tag_spiked = pop @merged; - $tag_last = pop @merged; - $tag_first = shift @merged; - is ($tag_zero->rpt_list, '25846:1:0;25846:2:0;25846:3:0;25846:4:0', - 'rpt list for tag zero object'); - is ($tag_spiked->rpt_list, '25846:1:888;25846:2:888;25846:3:888;25846:4:888', - 'rpt list for spiked in tag object'); - is ($tag_last->rpt_list, '25846:1:21;25846:2:21;25846:3:21;25846:4:21', - 'rpt list for tag 21 object'); - is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1', - 'rpt list for tag 1 object'); - - my $expected = { - '25846:1:0;25846:2:0;25846:3:0;25846:4:0' => { - 'sample_id' => undef, - 'sample_name' => undef, - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 5318, - 'study_name' => 'NovaSeq testing', - 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', - 'library_id' => undef, - 'library_name' => undef, - 'library_type' => 'Standard', - 'default_tag_sequence' => undef, - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }, - '25846:1:888;25846:2:888;25846:3:888;25846:4:888' => { - 'sample_id' => '1255141', - 'sample_name' => 'phiX_for_spiked_buffers', - 'sample_common_name' => undef, - 'study_id' => 198, - 'study_name' => 'Illumina Controls', - 'reference_genome' => undef, - 'library_id' => '17883061', - 'library_name' => '17883061', - 'library_type' => undef, - 'default_tag_sequence' => 'ACAACGCAATC', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }, - '25846:1:21;25846:2:21;25846:3:21;25846:4:21' => { - 'sample_id' => '3681772', - 'sample_name' => '5318STDY7462477', - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 5318, - 'study_name' => 'NovaSeq testing', - 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', - 'library_id' => '21059089', - 'library_name' => '21059089', - 'library_type' => 'Standard', - 'default_tag_sequence' => 'TCGAGCGT', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }, - '25846:1:1;25846:2:1;25846:3:1;25846:4:1' => { - 'sample_id' => '3681752', - 'sample_name' => '5318STDY7462457', - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 5318, - 'study_name' => 'NovaSeq testing', - 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', - 'library_id' => '21059039', - 'library_name' => '21059039', - 'library_type' => 'Standard', - 'default_tag_sequence' => 'ATCACGTT', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - } - }; - - for my $o (($tag_zero, $tag_spiked, $tag_first, $tag_last)) { - my $rpt_list = $o->rpt_list; - ok (!defined $o->id_run, "id_run not defined for $rpt_list"); - for my $method ( qw/ - sample_id sample_name sample_common_name - study_id study_name reference_genome - library_id library_name library_type - default_tag_sequence - /) { - is ($o->$method, $expected->{$rpt_list}->{$method}, "$method for $rpt_list"); - } - ok ($o->study_alignments_in_bam, "alignment true for $rpt_list"); - ok (!$o->study_contains_nonconsented_human, "nonconsented_human false for $rpt_list"); - } - - ok ($tag_spiked->is_phix_spike, 'is phix spike'); - ok (!$tag_first->is_phix_spike, 'is not phix spike'); - ok (!$tag_zero->is_phix_spike, 'is not phix spike'); - - is (join(q[:], $tag_zero->study_names), 'Illumina Controls:NovaSeq testing', - 'study names including spiked phix'); - is (join(q[:], $tag_zero->study_names(1)), 'Illumina Controls:NovaSeq testing', - 'sudy names including spiked phix'); - is (join(q[:], $tag_zero->study_names(0)), 'NovaSeq testing', - 'study names excluding spiked phix'); - - my @sample_names = qw/ - 5318STDY7462457 5318STDY7462458 5318STDY7462459 5318STDY7462460 5318STDY7462461 - 5318STDY7462462 5318STDY7462463 5318STDY7462464 5318STDY7462465 5318STDY7462466 - 5318STDY7462467 5318STDY7462468 5318STDY7462469 5318STDY7462470 5318STDY7462471 - 5318STDY7462472 5318STDY7462473 5318STDY7462474 5318STDY7462475 5318STDY7462476 - 5318STDY7462477 /; - - is (join(q[:], $tag_zero->sample_names(0)), join(q[:], @sample_names), - 'sample names excluding spiked phix'); - push @sample_names, 'phiX_for_spiked_buffers'; - is (join(q[:], $tag_zero->sample_names()), join(q[:], @sample_names), - 'sample names including spiked phix'); - is (join(q[:], $tag_zero->sample_names(1)), join(q[:], @sample_names), - 'sample names including spiked phix'); -}; - -subtest 'Aggregation across lanes for non-pools' => sub { - plan tests => 13; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_rapidrun_nopool.csv'; - my @merged = st::api::lims->new(id_run => 22672)->aggregate_xlanes(); - - my $l = $merged[0]; - is (scalar @merged, 1, 'one object returned'); - is ($l->rpt_list, '22672:1;22672:2', 'correct rpt_list'); - ok (!defined $l->id_run, "id_run not defined"); - ok (!$l->is_phix_spike, 'is not phix spike'); - - my $expected = { - 'sample_id' => '2917461', - 'sample_name' => '4600STDY6702635', - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 4600, - 'study_name' => 'Osteosarcoma_WGBS', - 'reference_genome' => 'Not suitable for alignment', - 'library_id' => '18914827', - 'library_name' => '18914827', - 'library_type' => 'Bisulphite pre quality controlled', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }; - - for my $method ( qw/ - sample_id sample_name sample_common_name - study_id study_name reference_genome - library_id library_name library_type - /) { - is ($l->$method, $expected->{$method}, "$method"); - } -}; - -subtest 'Aggregation across lanes for a tag' => sub { - plan tests => 13; - - local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; - - my $l = st::api::lims->new(rpt_list => '25846:1:1;25846:2:1'); - - my $e = qr/id_run and position are expected as arguments/; - throws_ok { $l->create_lane_object() } $e, 'no arguments - error'; - throws_ok { $l->create_lane_object(1) } $e, 'one argument - error'; - throws_ok { $l->create_lane_object(1, 0) } $e, - 'one of argument is false - error'; - - for my $p ((1,2)) { - my $lane_l = $l->create_lane_object(25846, $p); - is ($lane_l->id_run, 25846, 'run id is 25846'); - is ($lane_l->position, $p, "position is $p"); - is ($lane_l->rpt_list, undef, 'rpt_list is undefined'); - is ($lane_l->tag_index, undef, 'tag index is undefined'); - ok ($lane_l->is_pool, 'the entity is a pool'); - } -}; - subtest 'Creating tag zero object' => sub { plan tests => 4; From 0127b1829a24368f6c65cd0efeda85c5150e44e3 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 14 Nov 2023 16:02:34 +0000 Subject: [PATCH 26/35] Added tests for merging by library. Also refactored the method itself. --- MANIFEST | 1 + lib/st/api/lims.pm | 169 ++++++--- t/40-st-lims-merge.t | 442 ++++++++++++++++++----- t/40-st-lims.t | 1 - t/data/samplesheet/samplesheet_47995.csv | 184 ++++++++++ 5 files changed, 650 insertions(+), 147 deletions(-) create mode 100644 t/data/samplesheet/samplesheet_47995.csv diff --git a/MANIFEST b/MANIFEST index b06146ca..cf8ab46b 100644 --- a/MANIFEST +++ b/MANIFEST @@ -670,6 +670,7 @@ t/data/run_params/RunParameters.novaseq.xp.lite.xml t/data/samplesheet/samplesheet_7753.csv t/data/samplesheet/samplesheet_27483.csv t/data/samplesheet/samplesheet_33990.csv +t/data/samplesheet/samplesheet_47995.csv t/data/samplesheet/4pool4libs_extended.csv t/data/samplesheet/6946_extended.csv t/data/samplesheet/7007_extended.csv diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 1b3fa7bd..927742f5 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -11,6 +11,7 @@ use Class::Load qw/load_class/; use npg_tracking::util::types; use npg_tracking::glossary::rpt; +use npg_tracking::glossary::composition::factory::rpt_list; our $VERSION = '0'; @@ -63,6 +64,8 @@ Readonly::Scalar my $DEFAULT_DRIVER_TYPE => $SAMPLESHEET_DRIVER_TYPE; Readonly::Scalar my $DUAL_INDEX_TAG_LENGTH => 16; +Readonly::Scalar my $TAG_INDEX_4_UNDEFINED => -1; + Readonly::Hash my %METHODS_PER_CATEGORY => { 'primary' => [qw/ tag_index position @@ -912,84 +915,158 @@ sub aggregate_xlanes { =head2 aggregate_libraries +Given a list of lane-level C objects, finds their children, +which can be merged and analysed together across all or some of the lanes. +If children are not present, considers lane-level object as a single +library. + +All argument lane objects should belong to the same run. It is assumed that +they all use the same C driver type. + +Returns two lists of objects, one for merged entities and one for singletons, +which are wrapped into a dictionary. Either of these lists can be empty. Both +of the lists are guaranteed not to be empty at the same time. + +Tag zero objects are neither added nor explicitly removed. Objects for +spiked-in controls (if present) are always added to the list of singletons. + +The lists of singletons and merges are returned as sorted lists. For a given +set of input lane-level C objects the same lists are always +returned. + +Criteria for entities to be eligible for a merge: + they are not controls, + they belong to the same library, + they share the same tag index, + they belong to different lanes, one per lane, + they belong to the same study. + +This method can be used both as instance and as a class method. + + my $all_lims = st::api::lims->aggregate_libraries($run_lims->children()); + for my $l (@{$all_lims->{'singles'}}) { + print 'No merge for ' . $l->to_string; + } + for my $l (@{$all_lims->{'merges'}}) { + print 'Merged entity ' . $l->to_string; + } + =cut + sub aggregate_libraries() { my ($self, $lane_lims_array) = @_; - my @id_runs = uniq map { $_->id_run } @{$lane_lims_array}; - if (@id_runs != 1) { - croak 'Multiple run IDs in a potential library merge'; - } + # This restriction might be lifted in future. + _check_value_is_unique('id_run', 'run IDs', $lane_lims_array); - my $all_lims_objects = {}; my $lims_objects_by_library = {}; - + my @singles = (); my @all_single_lims_objs = map { $_->is_pool ? $_->children() : $_ } @{$lane_lims_array}; - foreach my $obj (@all_single_lims_objs) { - if ($obj->is_control()) { # Do not merge spiked PhiX libraries. - push @{$all_lims_objects->{'single'}}, $obj; + if ($obj->is_control()) { + push @singles, $obj; } else { push @{$lims_objects_by_library->{$obj->library_id}}, $obj; } } - my $merge_set = {}; - - # Do not use $self for this to retain ability to use this method as a class - # method. + # Get the common st::api::lims driver arguments, which will be used + # to create objects for merged entities. + # Do not use $self for copying the driver arguments in order to retain + # ability to use this method as a class method. my %init = %{$lane_lims_array->[0]->_driver_arguments()}; + delete $init{position}; + delete $init{id_run}; + my $merges = {}; + my $lane_set_delim = q[,]; foreach my $library_id (keys %{$lims_objects_by_library}) { my @lib_lims = @{$lims_objects_by_library->{$library_id}}; if (@lib_lims == 1) { - push @{$all_lims_objects->{'single'}}, $lib_lims[0]; + push @singles, @lib_lims; } else { - my @study_ids = uniq map { $_->study_id } @lib_lims; - if (@study_ids != 1) { - croak 'Multiple studies in a potential merge'; - } - my @tag_indexes = - uniq - map { defined $_->tag_index ? $_->tag_index : 'undefined' } - @lib_lims; - if (@tag_indexes != 1) { - croak 'Inconsistent tag indexes in a potential merge'; - } - my @lanes = uniq map {$_->position} @lib_lims; - if (@lanes != @lib_lims) { - croak 'Intra-lane merge is detected in a potential merge'; + _check_merge_correctness(\@lib_lims); + my $lane_set = join $lane_set_delim, + sort { $a <=> $b } map { $_->position } @lib_lims; + my $tag_index = $lib_lims[0]->tag_index ; + if (!defined $tag_index) { + $tag_index = $TAG_INDEX_4_UNDEFINED; } - my $lane_set = join q[,], @lanes; - $all_lims_objects->{'merges'}->{$lane_set}->{$tag_indexes[0]} = - __PACKAGE__->new( - %init, - rpt_list => npg_tracking::glossary::rpt->deflate_rpts(\@lib_lims) - ); + ##### + # rpt_list which we use to instantiate the object below has to be + # ordered correctly. Wrong order might not change the properties of + # the resulting st::api::lims object. However, difficult to track + # bugs might result in a situation when the value of this + # attribute for the object itself and for the composition object + # for this object differs. + my $rpt_list = npg_tracking::glossary::rpt->deflate_rpts(\@lib_lims); + $rpt_list = npg_tracking::glossary::composition::factory::rpt_list + ->new(rpt_list => $rpt_list)->create_composition() + ->freeze2rpt(); + $merges->{$lane_set}->{$tag_index} = __PACKAGE__->new( + %init, rpt_list => $rpt_list + ); } } - # Lane sets should not intersect. - my @positions = - map { (split /,/smx, $_) } - keys %{$all_lims_objects->{'merges'}}; - if (@positions != uniq @positions) { + # Lane sets should not intersect. Error if a lane belongs to multiple sets. + my @all_lanes_in_merged_sets = map { (split /$lane_set_delim/smx, $_) } + keys %{$merges}; + if (@all_lanes_in_merged_sets != uniq @all_lanes_in_merged_sets) { croak 'No clean split between lanes in potential merges'; } - # Within each set sort LIMS objects by tag index and keep - # the sorted list. - foreach my $lane_set ( keys %{$all_lims_objects->{'merges'}} ) { - my @sorted_lims_onjects = - map {$all_lims_objects->{'merges'}->{$lane_set}->{$_}} - (sort { $a <=> $b } keys %{$all_lims_objects->{'merges'}->{$lane_set}}); - $all_lims_objects->{'merges'}->{$lane_set} = \@sorted_lims_onjects; + my $all_lims_objects = {'singles' => [], 'merges' => []}; + # Arrange in a predictable consistent orger. + foreach my $lane_set ( sort keys %{$merges} ) { + my @tag_indexes = sort { $a <=> $b } keys %{$merges->{$lane_set}}; + push @{$all_lims_objects->{'merges'}}, + (map { $merges->{$lane_set}->{$_} } @tag_indexes); + } + $all_lims_objects->{'singles'} = [ + sort {##no critic (BuiltinFunctions::ProhibitReverseSortBlock BuiltinFunctions::RequireSimpleSortBlock) + my $index_a = defined $a->tag_index ? + $a->tag_index : $TAG_INDEX_4_UNDEFINED; + my $index_b = defined $b->tag_index ? + $b->tag_index : $TAG_INDEX_4_UNDEFINED; + $a->position <=> $b->position || $index_a <=> $index_b + } + @singles + ]; + + # Sanity check. + my $num_objects = @{$all_lims_objects->{'merges'}} + + @{$all_lims_objects->{'singles'}}; + if ($num_objects == 0) { + croak 'Invalid aggregation by library, no objects returned'; } return $all_lims_objects; } +sub _check_merge_correctness{ + my $lib_lims = shift; + my @lanes = uniq map {$_->position} @{$lib_lims}; + if (@lanes != @{$lib_lims}) { + croak 'Intra-lane merge is detected'; + } + _check_value_is_unique('study_id', 'studies', $lib_lims); + _check_value_is_unique('tag_index', 'tag indexes', $lib_lims); + return; +} + +sub _check_value_is_unique { + my ($method_name, $property_name, $objects) = @_; + my @values = uniq + map { defined $_->$method_name ? $_->$method_name : 'undefined' } + @{$objects}; + if (@values != 1) { + croak "Multiple $property_name in a potential merge by library"; + } + return; +} + =head2 create_tag_zero_object Using id_run and position values of this object, creates and returns diff --git a/t/40-st-lims-merge.t b/t/40-st-lims-merge.t index 01bc15e3..78f8cf8c 100644 --- a/t/40-st-lims-merge.t +++ b/t/40-st-lims-merge.t @@ -1,12 +1,18 @@ use strict; use warnings; -use Test::More tests => 4; +use Test::More tests => 9; use Test::Exception; +use List::MoreUtils qw/all none/; +use File::Slurp; +use File::Temp qw/tempdir/; +use_ok('npg_tracking::glossary::rpt'); use_ok('st::api::lims'); +my $tmp_dir = tempdir( CLEANUP => 1 ); + subtest 'Aggregation across lanes for pools' => sub { - plan tests => 85; + plan tests => 82; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; @@ -81,81 +87,11 @@ subtest 'Aggregation across lanes for pools' => sub { 'rpt list for tag 21 object'); is ($tag_first->rpt_list, '25846:1:1;25846:2:1;25846:3:1;25846:4:1', 'rpt list for tag 1 object'); + ok ((none {defined $_->id_run} ($tag_zero, $tag_spiked, $tag_first, $tag_last)), + "id_run not defined"); - my $expected = { - '25846:1:0;25846:2:0;25846:3:0;25846:4:0' => { - 'sample_id' => undef, - 'sample_name' => undef, - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 5318, - 'study_name' => 'NovaSeq testing', - 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', - 'library_id' => undef, - 'library_name' => undef, - 'library_type' => 'Standard', - 'default_tag_sequence' => undef, - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }, - '25846:1:888;25846:2:888;25846:3:888;25846:4:888' => { - 'sample_id' => '1255141', - 'sample_name' => 'phiX_for_spiked_buffers', - 'sample_common_name' => undef, - 'study_id' => 198, - 'study_name' => 'Illumina Controls', - 'reference_genome' => undef, - 'library_id' => '17883061', - 'library_name' => '17883061', - 'library_type' => undef, - 'default_tag_sequence' => 'ACAACGCAATC', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }, - '25846:1:21;25846:2:21;25846:3:21;25846:4:21' => { - 'sample_id' => '3681772', - 'sample_name' => '5318STDY7462477', - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 5318, - 'study_name' => 'NovaSeq testing', - 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', - 'library_id' => '21059089', - 'library_name' => '21059089', - 'library_type' => 'Standard', - 'default_tag_sequence' => 'TCGAGCGT', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }, - '25846:1:1;25846:2:1;25846:3:1;25846:4:1' => { - 'sample_id' => '3681752', - 'sample_name' => '5318STDY7462457', - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 5318, - 'study_name' => 'NovaSeq testing', - 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', - 'library_id' => '21059039', - 'library_name' => '21059039', - 'library_type' => 'Standard', - 'default_tag_sequence' => 'ATCACGTT', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - } - }; + _compare_properties([$tag_first, $tag_last, $tag_zero, $tag_spiked]); - for my $o (($tag_zero, $tag_spiked, $tag_first, $tag_last)) { - my $rpt_list = $o->rpt_list; - ok (!defined $o->id_run, "id_run not defined for $rpt_list"); - for my $method ( qw/ - sample_id sample_name sample_common_name - study_id study_name reference_genome - library_id library_name library_type - default_tag_sequence - /) { - is ($o->$method, $expected->{$rpt_list}->{$method}, "$method for $rpt_list"); - } - ok ($o->study_alignments_in_bam, "alignment true for $rpt_list"); - ok (!$o->study_contains_nonconsented_human, "nonconsented_human false for $rpt_list"); - } - ok ($tag_spiked->is_phix_spike, 'is phix spike'); ok (!$tag_first->is_phix_spike, 'is not phix spike'); ok (!$tag_zero->is_phix_spike, 'is not phix spike'); @@ -184,38 +120,16 @@ subtest 'Aggregation across lanes for pools' => sub { }; subtest 'Aggregation across lanes for non-pools' => sub { - plan tests => 13; + plan tests => 14; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/test40_lims/samplesheet_rapidrun_nopool.csv'; my @merged = st::api::lims->new(id_run => 22672)->aggregate_xlanes(); - - my $l = $merged[0]; is (scalar @merged, 1, 'one object returned'); + my $l = $merged[0]; is ($l->rpt_list, '22672:1;22672:2', 'correct rpt_list'); ok (!defined $l->id_run, "id_run not defined"); ok (!$l->is_phix_spike, 'is not phix spike'); - - my $expected = { - 'sample_id' => '2917461', - 'sample_name' => '4600STDY6702635', - 'sample_common_name' => 'Homo sapiens', - 'study_id' => 4600, - 'study_name' => 'Osteosarcoma_WGBS', - 'reference_genome' => 'Not suitable for alignment', - 'library_id' => '18914827', - 'library_name' => '18914827', - 'library_type' => 'Bisulphite pre quality controlled', - 'study_alignments_in_bam' => 1, - 'study_contains_nonconsented_human' => 0 - }; - - for my $method ( qw/ - sample_id sample_name sample_common_name - study_id study_name reference_genome - library_id library_name library_type - /) { - is ($l->$method, $expected->{$method}, "$method"); - } + _compare_properties_2($l); }; subtest 'Aggregation across lanes for a tag' => sub { @@ -241,4 +155,332 @@ subtest 'Aggregation across lanes for a tag' => sub { } }; +subtest 'Error conditions in aggregation by library' => sub { + plan tests => 4; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + my @lane_lims = st::api::lims->new(id_run => 25846)->children; + my @mixed_lanes = ($lane_lims[0]); + my $ss_47995_path = 't/data/samplesheet/samplesheet_47995.csv'; + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $ss_47995_path; + @lane_lims = st::api::lims->new(id_run => 47995)->children; + push @mixed_lanes, $lane_lims[0]; + + throws_ok { st::api::lims->aggregate_libraries(\@mixed_lanes) } + qr/Multiple run IDs in a potential merge by library/, + 'data for a single run is expected'; + + my $lane_1_lib = ($lane_lims[0]->children())[0]; + my $lane_2_lib = ($lane_lims[1]->children())[0]; + throws_ok { + st::api::lims->aggregate_libraries([$lane_1_lib, $lane_2_lib, $lane_1_lib]) + } qr/Intra-lane merge is detected/, 'merges should be between lanes'; + + my $content = read_file($ss_47995_path); + $content =~ s/,6751,/,6752,/; # One change of the study id. + my $file_path = join q[/], $tmp_dir, 'samplesheet_multi_study.csv'; + write_file($file_path, $content); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $file_path; + @lane_lims = st::api::lims->new(id_run => 47995)->children; + throws_ok { st::api::lims->aggregate_libraries(\@lane_lims) } + qr/Multiple studies in a potential merge by library/, + 'can only merge libraries that belong to the same study'; + + $content = read_file($ss_47995_path); + # Make library id of tag 1 lane 1 the same as for tag 2 lane 3. + $content =~ s/1,65934716,/1,69723083,/; + # Change study id for all tags of lane 3 to be the same as in lane 1. + $content =~ s/,6050,/,6751,/g; + $file_path = join q[/], $tmp_dir, 'samplesheet_multi_tag.csv'; + write_file($file_path, $content); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $file_path; + @lane_lims = st::api::lims->new(id_run => 47995)->children; + throws_ok { st::api::lims->aggregate_libraries(\@lane_lims) } + qr/Multiple tag indexes in a potential merge by library/, + 'can only merge libraries with teh same tag index'; +}; + +subtest 'Aggregation by library for a NovaSeq standard flowcell' => sub { + plan tests => 101; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/test40_lims/samplesheet_novaseq4lanes.csv'; + # All lanes of this runs can be merged together. + # The pool contains a spiked-in control. + + my $id_run = 25846; + my @lane_lims = st::api::lims->new(id_run => $id_run)->children; + my $lims = st::api::lims->aggregate_libraries(\@lane_lims); + + for my $key_name (qw/singles merges/) { + ok (exists $lims->{$key_name}, "entry for $key_name exists"); + is (ref $lims->{$key_name}, 'ARRAY', 'the value is an array'); + } + is (keys %{$lims}, 2, 'no unexpected keys'); + is (@{$lims->{'singles'}}, 4, 'list of singles contains 4 objects'); + is (@{$lims->{'merges'}}, 21, 'list of merges contains 21 objects'); + + ok ( (all { $_->is_control } @{$lims->{'singles'}}), + 'all singles are spiked-in controls'); + ok ((none { defined $_->rpt_list } @{$lims->{'singles'}}), + 'rpt_list value is not defined for singles'); + ok ((all { $_->id_run == $id_run } @{$lims->{'singles'}}), + 'id_run is set correctly for singles'); + ok ((all { $_->tag_index == 888 } @{$lims->{'singles'}}), + 'tag_index is set correctly for singles'); + is ('1,2,3,4', join(q[,], map { $_->position } @{$lims->{'singles'}}), + 'objects are ordered in position acsending order'); + + my @rpt_lists = map { $_->rpt_list } @{$lims->{'merges'}}; + my @expected_rpt_lists = _generate_rpt_lists($id_run, [(1 .. 4)], [(1 .. 21)]); + is_deeply (\@rpt_lists, \@expected_rpt_lists, + 'merges list - correct object, correct sort order'); + + for my $method_name (qw/id_run position tag_index/) { + ok ((none { defined $_->$method_name } @{$lims->{'merges'}}), + "$method_name is not defined"); + } + ok ((all { $_->driver_type eq 'samplesheet' } @{$lims->{'merges'}}), + 'driver type is correct'); + + _compare_properties([$lims->{'merges'}->[0], $lims->{'merges'}->[20]]); + + # Select two lanes out of four. + $lims = st::api::lims->aggregate_libraries([$lane_lims[0], $lane_lims[2]]); + is (@{$lims->{'singles'}}, 2, 'list of singles contains 2 objects'); + is (@{$lims->{'merges'}}, 21, 'list of merges contains 21 objects'); + @rpt_lists = map { $_->rpt_list } @{$lims->{'merges'}}; + @expected_rpt_lists = _generate_rpt_lists($id_run, [1, 3], [(1 .. 21)]); + is_deeply (\@rpt_lists, \@expected_rpt_lists, + 'merges list - correct object, correct sort order'); + _compare_properties([$lims->{'merges'}->[0], $lims->{'merges'}->[20]]); + + # Select one lane only, No 2. Invoke the method on an instance. + my $lane = $lane_lims[1]; + $lims = $lane->aggregate_libraries([$lane]); + is (@{$lims->{'singles'}}, 22, 'list of singles contains 22 objects'); + is (@{$lims->{'merges'}}, 0, 'list of merges is empty'); + ok ((none { defined $_->rpt_list } @{$lims->{'singles'}}), + 'rpt_list value is not defined for singles'); + ok ((all { $_->id_run == $id_run && $_->position == 2} @{$lims->{'singles'}}), + 'id_run and position are set correctly for singles'); + my @tag_indexes = map { $_->tag_index } @{$lims->{'singles'}}; + is_deeply (\@tag_indexes, [(1 .. 21, 888)], + 'tag indexes are set correctly, correct sort order'); + ok ($lims->{'singles'}->[21]->is_control, 'tag 888 is flagged as control'); + ok ((none { $lims->{'singles'}->[$_]->is_control } (0 .. 20)), + 'all other objects are not marked as controls'); + _compare_properties([$lims->{'singles'}->[0], $lims->{'singles'}->[20]]); + + # Remove spiked-in controls from the samplesheet. + my @lines = grep { $_ !~ /phiX_for_spiked_buffers/ } + read_file($ENV{NPG_CACHED_SAMPLESHEET_FILE}); + my $file_path = join q[/], $tmp_dir, 'samplesheet.csv'; + write_file($file_path, @lines); + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = $file_path; + @lane_lims = st::api::lims->new(id_run => $id_run)->children; + $lims = st::api::lims->aggregate_libraries(\@lane_lims); + is (@{$lims->{'singles'}}, 0, 'list of singles is empty'); + is (@{$lims->{'merges'}}, 21, 'list of merges contains 21 objects'); +}; + +subtest 'Aggregation by library for non-pools' => sub { + plan tests => 15; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/test40_lims/samplesheet_rapidrun_nopool.csv'; + my @lane_lims = st::api::lims->new(id_run => 22672)->children(); + my $lims = st::api::lims->aggregate_libraries(\@lane_lims); + is (@{$lims->{'singles'}}, 0, 'list of singles is empty'); + is (@{$lims->{'merges'}}, 1, 'list of merges contains one object'); + my $l = $lims->{'merges'}->[0]; + is ($l->rpt_list, '22672:1;22672:2', 'correct rpt_list'); + _compare_properties_2($l); + + $lims = st::api::lims->aggregate_libraries([$lane_lims[0]]); + is (@{$lims->{'singles'}}, 1, 'list of singles contains one object'); + is (@{$lims->{'merges'}}, 0, 'list of merges is empty'); +}; + +subtest 'Multiple lane sets in aggregation by library' => sub { + plan tests => 11; + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + 't/data/samplesheet/samplesheet_47995.csv'; + my $id_run = 47995; + my @lane_lims = st::api::lims->new(id_run => $id_run)->children(); + # Reverse the order of the argument list. + my $lims = st::api::lims->aggregate_libraries([reverse @lane_lims]); + + is (@{$lims->{'singles'}}, 8, 'list of singles contains 8 objects'); + ok ((all {$_->is_control} @{$lims->{'singles'}}), 'all singles are controls'); + ok ((all {$_->tag_index == 888} @{$lims->{'singles'}}), 'all singles have tag 888'); + is_deeply ([(1 .. 8)], [map {$_->position} @{$lims->{'singles'}}], + 'correct sort order'); + + is (@{$lims->{'merges'}}, 87, 'list of merges contains 87 objects'); + my %lanes_tags = ( + '1,2' => [(1 .. 17)], + '3,4' => [(1 .. 10)], + '5,6' => [(1 .. 22)], + '7,8' => [(1 .. 38)], + ); + my @expected_rpt_lists = (); + for my $lane_set (sort keys %lanes_tags) { + my @lanes = split q[,], $lane_set; + push @expected_rpt_lists, + _generate_rpt_lists($id_run, \@lanes, $lanes_tags{$lane_set}); + } + my @rpt_lists = map { $_->rpt_list } @{$lims->{'merges'}}; + is_deeply (\@rpt_lists, \@expected_rpt_lists, + 'merges list - correct object, correct sort order'); + + # Two lanes to be merged (1, 2), two lanes (4, 8) as is. + $lims = st::api::lims->aggregate_libraries( + [$lane_lims[3], $lane_lims[1], $lane_lims[0], $lane_lims[7]]); + + my $expected_num_singles = scalar @{$lanes_tags{'3,4'}} + + scalar @{$lanes_tags{'7,8'}} + + 4; # Controls for lanes 1,2,4,8. + is (@{$lims->{'singles'}}, $expected_num_singles, + "list of singles contains $expected_num_singles objects"); + is (scalar (grep {$_->is_control} @{$lims->{'singles'}}), 4, + '4 singles are controls'); + + @expected_rpt_lists = map {join q[:], $id_run, $_, 888} (1,2); + push @expected_rpt_lists, + _generate_rpt_lists($id_run, [4], $lanes_tags{'3,4'}), "${id_run}:4:888"; + push @expected_rpt_lists, + _generate_rpt_lists($id_run, [8], $lanes_tags{'7,8'}), "${id_run}:8:888"; + @rpt_lists = (); + foreach my $l (@{$lims->{'singles'}}) { + push @rpt_lists, npg_tracking::glossary::rpt->deflate_rpts([$l]); + } + is_deeply (\@rpt_lists, \@expected_rpt_lists, + 'singles list - correct object, correct sort order'); + + is (@{$lims->{'merges'}}, 17, 'list of merges contains 17 objects'); + @expected_rpt_lists = _generate_rpt_lists($id_run, [1,2], $lanes_tags{'1,2'}); + @rpt_lists = map { $_->rpt_list } @{$lims->{'merges'}}; + is_deeply (\@rpt_lists, \@expected_rpt_lists, + 'merges list - correct object, correct sort order'); +}; + +sub _generate_rpt_lists { + my ($id_run, $positions, $tag_indexes) = @_; + my @expected_rpt_lists = (); + foreach my $tag_index (@{$tag_indexes}) { + my @rpt_list = (); + for my $position (@{$positions}) { + push @rpt_list, join q[:], $id_run, $position, $tag_index; + } + push @expected_rpt_lists, join q[;], @rpt_list; + } + return @expected_rpt_lists; +} + +sub _compare_properties { + my $lims_objects = shift; + + my $expected_props = [ + { + 'sample_id' => '3681752', + 'sample_name' => '5318STDY7462457', + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 5318, + 'study_name' => 'NovaSeq testing', + 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', + 'library_id' => '21059039', + 'library_name' => '21059039', + 'library_type' => 'Standard', + 'default_tag_sequence' => 'ATCACGTT', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }, + { + 'sample_id' => '3681772', + 'sample_name' => '5318STDY7462477', + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 5318, + 'study_name' => 'NovaSeq testing', + 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', + 'library_id' => '21059089', + 'library_name' => '21059089', + 'library_type' => 'Standard', + 'default_tag_sequence' => 'TCGAGCGT', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }, + { + 'sample_id' => undef, + 'sample_name' => undef, + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 5318, + 'study_name' => 'NovaSeq testing', + 'reference_genome' => 'Homo_sapiens (1000Genomes_hs37d5 + ensembl_75_transcriptome)', + 'library_id' => undef, + 'library_name' => undef, + 'library_type' => 'Standard', + 'default_tag_sequence' => undef, + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + }, + { + 'sample_id' => '1255141', + 'sample_name' => 'phiX_for_spiked_buffers', + 'sample_common_name' => undef, + 'study_id' => 198, + 'study_name' => 'Illumina Controls', + 'reference_genome' => undef, + 'library_id' => '17883061', + 'library_name' => '17883061', + 'library_type' => undef, + 'default_tag_sequence' => 'ACAACGCAATC', + 'study_alignments_in_bam' => 1, + 'study_contains_nonconsented_human' => 0 + } + ]; + + my $num_objects = @{$lims_objects}; + for my $i ((0 .. $num_objects-1)) { + my $o = $lims_objects->[$i]; + my $description = $o->rpt_list ? $o->rpt_list : $o->to_string; + my $expected = $expected_props->[$i]; + for my $method ( qw/ + sample_id sample_name sample_common_name + study_id study_name reference_genome + library_id library_name library_type + default_tag_sequence study_alignments_in_bam + /) { + is ($o->$method, $expected->{$method}, "$method for $description"); + } + ok (!$o->study_contains_nonconsented_human, "nonconsented_human false for $description"); + } + + return; +} + +sub _compare_properties_2 { + my $obj = shift; + my $rpt_list = $obj->rpt_list; + my %expected = ( + 'sample_id' => '2917461', + 'sample_name' => '4600STDY6702635', + 'sample_common_name' => 'Homo sapiens', + 'study_id' => 4600, + 'study_name' => 'Osteosarcoma_WGBS', + 'reference_genome' => 'Not suitable for alignment', + 'library_id' => '18914827', + 'library_name' => '18914827', + 'library_type' => 'Bisulphite pre quality controlled', + 'study_alignments_in_bam' => 1, + ); + for my $method ( sort keys %expected) { + is ($obj->$method, $expected{$method}, "$method for $rpt_list"); + } + + return; +} + 1; diff --git a/t/40-st-lims.t b/t/40-st-lims.t index 37dba533..f659a86b 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -3,7 +3,6 @@ use warnings; use Test::More tests => 16; use Test::Exception; use Test::Warn; -use File::Temp qw/ tempdir /; use Moose::Meta::Class; my $num_delegated_methods = 45; diff --git a/t/data/samplesheet/samplesheet_47995.csv b/t/data/samplesheet/samplesheet_47995.csv new file mode 100644 index 00000000..e9b16751 --- /dev/null +++ b/t/data/samplesheet/samplesheet_47995.csv @@ -0,0 +1,184 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,65934716,EGAN00004177411,,CCTTCTCT,ATTGAGAG,TE-95148282,Targeted NanoSeq Pulldown Twist,CCTTCTCT,ATTGAGAG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934716,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177411,Normal,Homo sapiens,0,,,PD45703b_tds0003,8508809,0,6751STDY13219549,PD45703b_tds0003,,PD45703b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,1, +1,65934633,EGAN00004177412,,TTTGAGGG,CCCAATCA,TE-95148282,Targeted NanoSeq Pulldown Twist,TTTGAGGG,CCCAATCA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934633,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177412,Normal,Homo sapiens,0,,,PD45704b_tds0002,8508810,0,6751STDY13219550,PD45704b_tds0002,,PD45704b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,2, +1,65934645,EGAN00004177418,,GGCCTGGC,TTGCAATC,TE-95148282,Targeted NanoSeq Pulldown Twist,GGCCTGGC,TTGCAATC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934645,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177418,Normal,Homo sapiens,0,,,PD45704b_tds0003,8508815,0,6751STDY13219555,PD45704b_tds0003,,PD45704b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,3, +1,65934657,EGAN00004177402,,AAAGTGAA,ATGGCAGC,TE-95148282,Targeted NanoSeq Pulldown Twist,AAAGTGAA,ATGGCAGC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934657,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177402,Normal,Homo sapiens,0,,,PD43959b_tds0002,8508801,0,6751STDY13219541,PD43959b_tds0002,,PD43959b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,4, +1,65934669,EGAN00004177414,,ACTCGAAA,CACGCGAC,TE-95148282,Targeted NanoSeq Pulldown Twist,ACTCGAAA,CACGCGAC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934669,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177414,Normal,Homo sapiens,0,,,PD45707b_tds0002,8508812,0,6751STDY13219552,PD45707b_tds0002,,PD45707b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,5, +1,65934681,EGAN00004177417,,CGATTGCA,ACCCAGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,CGATTGCA,ACCCAGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934681,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177417,Normal,Homo sapiens,0,,,PD49159b_tds0002,8508816,0,6751STDY13219556,PD49159b_tds0002,,PD49159b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,6, +1,65934693,EGAN00004177419,,GTAAGCGA,GTTTGGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTAAGCGA,GTTTGGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934693,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177419,Normal,Homo sapiens,0,,,PD49134b_tds0002,8508817,0,6751STDY13219557,PD49134b_tds0002,,PD49134b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,7, +1,65934705,EGAN00004177400,,TTCTTCAG,ACCACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,TTCTTCAG,ACCACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934705,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177400,Normal,Homo sapiens,0,,,PD43957b_tds0002,8508799,0,6751STDY13219539,PD43957b_tds0002,,PD43957b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,8, +1,65934717,EGAN00004177407,,CGTGGATA,TTCCGGTG,TE-95148282,Targeted NanoSeq Pulldown Twist,CGTGGATA,TTCCGGTG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934717,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177407,Normal,Homo sapiens,0,,,PD43958b_tds0002,8508800,0,6751STDY13219540,PD43958b_tds0002,,PD43958b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,9, +1,65934634,EGAN00004177403,,CACTTTGC,AGTCGATG,TE-95148282,Targeted NanoSeq Pulldown Twist,CACTTTGC,AGTCGATG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934634,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177403,Normal,Homo sapiens,0,,,PD43960b_tds0002,8508802,0,6751STDY13219542,PD43960b_tds0002,,PD43960b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,10, +1,65934646,EGAN00004177404,,GTGTCGGT,GATGCGTC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGTCGGT,GATGCGTC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934646,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177404,Normal,Homo sapiens,0,,,PD43961b_tds0002,8508803,0,6751STDY13219543,PD43961b_tds0002,,PD43961b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,11, +1,65934658,EGAN00004177405,,ACGTAACA,ACATTCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,ACGTAACA,ACATTCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934658,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177405,Normal,Homo sapiens,0,,,PD43962b_tds0003,8508804,0,6751STDY13219544,PD43962b_tds0003,,PD43962b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,12, +1,65934670,EGAN00004177406,,CTTTCGAC,CAGACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,CTTTCGAC,CAGACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934670,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177406,Normal,Homo sapiens,0,,,PD43964b_tds0002,8508805,0,6751STDY13219545,PD43964b_tds0002,,PD43964b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,13, +1,65934682,EGAN00004177410,,GTGACCTA,ATAGCGTT,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGACCTA,ATAGCGTT,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934682,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177410,Normal,Homo sapiens,0,,,PD43965b_tds0002,8508806,0,6751STDY13219546,PD43965b_tds0002,,PD43965b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,14, +1,65934694,EGAN00004177408,,GTCCTAAC,TACGCCGA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTCCTAAC,TACGCCGA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934694,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177408,Normal,Homo sapiens,0,,,PD45701b_tds0002,8508807,0,6751STDY13219547,PD45701b_tds0002,,PD45701b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,15, +1,65934706,EGAN00004177413,,GTGCAGGG,AGTCTGCC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGCAGGG,AGTCTGCC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934706,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177413,Normal,Homo sapiens,0,,,PD45705b_tds0002,8508811,0,6751STDY13219551,PD45705b_tds0002,,PD45705b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,16, +1,65934718,EGAN00004177416,,TGCGGTGT,GCAACCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,TGCGGTGT,GCAACCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934718,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177416,Normal,Homo sapiens,0,,,PD49155b_tds0002,8508814,0,6751STDY13219554,PD49155b_tds0002,,PD49155b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,17, +1,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004573,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +2,65934716,EGAN00004177411,,CCTTCTCT,ATTGAGAG,TE-95148282,Targeted NanoSeq Pulldown Twist,CCTTCTCT,ATTGAGAG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934716,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177411,Normal,Homo sapiens,0,,,PD45703b_tds0003,8508809,0,6751STDY13219549,PD45703b_tds0003,,PD45703b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,1, +2,65934633,EGAN00004177412,,TTTGAGGG,CCCAATCA,TE-95148282,Targeted NanoSeq Pulldown Twist,TTTGAGGG,CCCAATCA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934633,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177412,Normal,Homo sapiens,0,,,PD45704b_tds0002,8508810,0,6751STDY13219550,PD45704b_tds0002,,PD45704b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,2, +2,65934645,EGAN00004177418,,GGCCTGGC,TTGCAATC,TE-95148282,Targeted NanoSeq Pulldown Twist,GGCCTGGC,TTGCAATC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934645,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177418,Normal,Homo sapiens,0,,,PD45704b_tds0003,8508815,0,6751STDY13219555,PD45704b_tds0003,,PD45704b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,3, +2,65934657,EGAN00004177402,,AAAGTGAA,ATGGCAGC,TE-95148282,Targeted NanoSeq Pulldown Twist,AAAGTGAA,ATGGCAGC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934657,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177402,Normal,Homo sapiens,0,,,PD43959b_tds0002,8508801,0,6751STDY13219541,PD43959b_tds0002,,PD43959b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,4, +2,65934669,EGAN00004177414,,ACTCGAAA,CACGCGAC,TE-95148282,Targeted NanoSeq Pulldown Twist,ACTCGAAA,CACGCGAC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934669,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177414,Normal,Homo sapiens,0,,,PD45707b_tds0002,8508812,0,6751STDY13219552,PD45707b_tds0002,,PD45707b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,5, +2,65934681,EGAN00004177417,,CGATTGCA,ACCCAGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,CGATTGCA,ACCCAGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934681,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177417,Normal,Homo sapiens,0,,,PD49159b_tds0002,8508816,0,6751STDY13219556,PD49159b_tds0002,,PD49159b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,6, +2,65934693,EGAN00004177419,,GTAAGCGA,GTTTGGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTAAGCGA,GTTTGGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934693,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177419,Normal,Homo sapiens,0,,,PD49134b_tds0002,8508817,0,6751STDY13219557,PD49134b_tds0002,,PD49134b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,7, +2,65934705,EGAN00004177400,,TTCTTCAG,ACCACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,TTCTTCAG,ACCACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934705,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177400,Normal,Homo sapiens,0,,,PD43957b_tds0002,8508799,0,6751STDY13219539,PD43957b_tds0002,,PD43957b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,8, +2,65934717,EGAN00004177407,,CGTGGATA,TTCCGGTG,TE-95148282,Targeted NanoSeq Pulldown Twist,CGTGGATA,TTCCGGTG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934717,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177407,Normal,Homo sapiens,0,,,PD43958b_tds0002,8508800,0,6751STDY13219540,PD43958b_tds0002,,PD43958b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,9, +2,65934634,EGAN00004177403,,CACTTTGC,AGTCGATG,TE-95148282,Targeted NanoSeq Pulldown Twist,CACTTTGC,AGTCGATG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934634,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177403,Normal,Homo sapiens,0,,,PD43960b_tds0002,8508802,0,6751STDY13219542,PD43960b_tds0002,,PD43960b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,10, +2,65934646,EGAN00004177404,,GTGTCGGT,GATGCGTC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGTCGGT,GATGCGTC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934646,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177404,Normal,Homo sapiens,0,,,PD43961b_tds0002,8508803,0,6751STDY13219543,PD43961b_tds0002,,PD43961b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,11, +2,65934658,EGAN00004177405,,ACGTAACA,ACATTCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,ACGTAACA,ACATTCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934658,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177405,Normal,Homo sapiens,0,,,PD43962b_tds0003,8508804,0,6751STDY13219544,PD43962b_tds0003,,PD43962b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,12, +2,65934670,EGAN00004177406,,CTTTCGAC,CAGACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,CTTTCGAC,CAGACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934670,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177406,Normal,Homo sapiens,0,,,PD43964b_tds0002,8508805,0,6751STDY13219545,PD43964b_tds0002,,PD43964b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,13, +2,65934682,EGAN00004177410,,GTGACCTA,ATAGCGTT,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGACCTA,ATAGCGTT,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934682,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177410,Normal,Homo sapiens,0,,,PD43965b_tds0002,8508806,0,6751STDY13219546,PD43965b_tds0002,,PD43965b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,14, +2,65934694,EGAN00004177408,,GTCCTAAC,TACGCCGA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTCCTAAC,TACGCCGA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934694,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177408,Normal,Homo sapiens,0,,,PD45701b_tds0002,8508807,0,6751STDY13219547,PD45701b_tds0002,,PD45701b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,15, +2,65934706,EGAN00004177413,,GTGCAGGG,AGTCTGCC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGCAGGG,AGTCTGCC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934706,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177413,Normal,Homo sapiens,0,,,PD45705b_tds0002,8508811,0,6751STDY13219551,PD45705b_tds0002,,PD45705b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,16, +2,65934718,EGAN00004177416,,TGCGGTGT,GCAACCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,TGCGGTGT,GCAACCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934718,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177416,Normal,Homo sapiens,0,,,PD49155b_tds0002,8508814,0,6751STDY13219554,PD49155b_tds0002,,PD49155b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,17, +2,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004574,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +3,69723082,6050STDY14354621,,TTGATTCC,AGAAGCCC,,Duplex-Seq,TTGATTCC,AGAAGCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723082,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296053,0,6050STDY14354621,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +3,69723083,6050STDY14354622,,CATCATTT,ACCTAACT,,Duplex-Seq,CATCATTT,ACCTAACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723083,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296054,0,6050STDY14354622,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +3,69723084,6050STDY14354623,,ATATGCGC,GCTAATTG,,Duplex-Seq,ATATGCGC,GCTAATTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723084,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296055,0,6050STDY14354623,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +3,69723085,6050STDY14354624,,GTAAATGC,GGTAGGTG,,Duplex-Seq,GTAAATGC,GGTAGGTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723085,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296056,0,6050STDY14354624,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +3,69723086,6050STDY14354625,,TTAGTAGA,AAATTCAC,,Duplex-Seq,TTAGTAGA,AAATTCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723086,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296057,0,6050STDY14354625,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +3,69723087,6050STDY14354626,,CTGATGCT,CTGGATTT,,Duplex-Seq,CTGATGCT,CTGGATTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723087,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296058,0,6050STDY14354626,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +3,69723088,6050STDY14354627,,CTTGCGTG,TACTGCCG,,Duplex-Seq,CTTGCGTG,TACTGCCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723088,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296059,0,6050STDY14354627,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +3,69723089,6050STDY14354628,,CTGTCACA,CATTTATC,,Duplex-Seq,CTGTCACA,CATTTATC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723089,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296060,0,6050STDY14354628,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +3,69723090,6050STDY14354629,,GCCTAGGG,AGTTGGAG,,Duplex-Seq,GCCTAGGG,AGTTGGAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723090,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296061,0,6050STDY14354629,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +3,69723091,6050STDY14354630,,CTTACTCA,TCTCGACC,,Duplex-Seq,CTTACTCA,TCTCGACC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723091,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296062,0,6050STDY14354630,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +3,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004575,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +4,69723082,6050STDY14354621,,TTGATTCC,AGAAGCCC,,Duplex-Seq,TTGATTCC,AGAAGCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723082,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296053,0,6050STDY14354621,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +4,69723083,6050STDY14354622,,CATCATTT,ACCTAACT,,Duplex-Seq,CATCATTT,ACCTAACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723083,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296054,0,6050STDY14354622,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +4,69723084,6050STDY14354623,,ATATGCGC,GCTAATTG,,Duplex-Seq,ATATGCGC,GCTAATTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723084,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296055,0,6050STDY14354623,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +4,69723085,6050STDY14354624,,GTAAATGC,GGTAGGTG,,Duplex-Seq,GTAAATGC,GGTAGGTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723085,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296056,0,6050STDY14354624,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +4,69723086,6050STDY14354625,,TTAGTAGA,AAATTCAC,,Duplex-Seq,TTAGTAGA,AAATTCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723086,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296057,0,6050STDY14354625,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +4,69723087,6050STDY14354626,,CTGATGCT,CTGGATTT,,Duplex-Seq,CTGATGCT,CTGGATTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723087,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296058,0,6050STDY14354626,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +4,69723088,6050STDY14354627,,CTTGCGTG,TACTGCCG,,Duplex-Seq,CTTGCGTG,TACTGCCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723088,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296059,0,6050STDY14354627,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +4,69723089,6050STDY14354628,,CTGTCACA,CATTTATC,,Duplex-Seq,CTGTCACA,CATTTATC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723089,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296060,0,6050STDY14354628,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +4,69723090,6050STDY14354629,,GCCTAGGG,AGTTGGAG,,Duplex-Seq,GCCTAGGG,AGTTGGAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723090,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296061,0,6050STDY14354629,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +4,69723091,6050STDY14354630,,CTTACTCA,TCTCGACC,,Duplex-Seq,CTTACTCA,TCTCGACC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723091,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296062,0,6050STDY14354630,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +4,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004576,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +5,69725419,6050STDY14355627,,CGGAGACA,ATGCGACT,,Duplex-Seq,CGGAGACA,ATGCGACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725419,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296963,0,6050STDY14355627,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +5,69725420,6050STDY14355628,,GTTAACGT,TCACAAAC,,Duplex-Seq,GTTAACGT,TCACAAAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725420,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296964,0,6050STDY14355628,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +5,69725421,6050STDY14355629,,CATTTATT,AGGAGAAA,,Duplex-Seq,CATTTATT,AGGAGAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725421,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296965,0,6050STDY14355629,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +5,69725422,6050STDY14355630,,TTAGCGCA,TCGGCAAA,,Duplex-Seq,TTAGCGCA,TCGGCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725422,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296966,0,6050STDY14355630,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +5,69725423,6050STDY14355631,,TATTCGTA,CTGAAAGA,,Duplex-Seq,TATTCGTA,CTGAAAGA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725423,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296967,0,6050STDY14355631,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_Matched,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +5,69725424,6050STDY14355632,,CTAACTAG,GAAAGGTA,,Duplex-Seq,CTAACTAG,GAAAGGTA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725424,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296968,0,6050STDY14355632,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +5,69725425,6050STDY14355633,,TTTGCAAA,ACACATAT,,Duplex-Seq,TTTGCAAA,ACACATAT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725425,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296969,0,6050STDY14355633,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +5,69725426,6050STDY14355634,,CTTAGAGT,GAACCCTG,,Duplex-Seq,CTTAGAGT,GAACCCTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725426,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296970,0,6050STDY14355634,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +5,69725427,6050STDY14355635,,GGTGGGAA,TAAACCCA,,Duplex-Seq,GGTGGGAA,TAAACCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725427,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296971,0,6050STDY14355635,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +5,69725428,6050STDY14355636,,CCTCCTAA,ATGCACTG,,Duplex-Seq,CCTCCTAA,ATGCACTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725428,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296972,0,6050STDY14355636,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +5,69725429,6050STDY14355637,,TTTCCAGT,ATGCCAAA,,Duplex-Seq,TTTCCAGT,ATGCCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725429,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296973,0,6050STDY14355637,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),11, +5,69725430,6050STDY14355638,,GATATGTG,CCTACTAA,,Duplex-Seq,GATATGTG,CCTACTAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725430,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296974,0,6050STDY14355638,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),12, +5,69725431,6050STDY14355639,,CATGAATC,ATAAACTT,,Duplex-Seq,CATGAATC,ATAAACTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725431,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296975,0,6050STDY14355639,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),13, +5,69725432,6050STDY14355640,,AGTAGTAG,AGGCCGTT,,Duplex-Seq,AGTAGTAG,AGGCCGTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725432,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296976,0,6050STDY14355640,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),14, +5,69725433,6050STDY14355641,,GAGGGCCG,ACCCTCCA,,Duplex-Seq,GAGGGCCG,ACCCTCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725433,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296977,0,6050STDY14355641,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),15, +5,69725434,6050STDY14355642,,TTGTCCAA,CGGATCCC,,Duplex-Seq,TTGTCCAA,CGGATCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725434,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296978,0,6050STDY14355642,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),16, +5,69725435,6050STDY14355643,,CGCAACTG,TGCCATCC,,Duplex-Seq,CGCAACTG,TGCCATCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725435,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296979,0,6050STDY14355643,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),17, +5,69725436,6050STDY14355644,,CATATTCT,CGGACAAG,,Duplex-Seq,CATATTCT,CGGACAAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725436,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296980,0,6050STDY14355644,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_Macthed,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),18, +5,69725437,6050STDY14355645,,GCGGAGAC,CATTGCAC,,Duplex-Seq,GCGGAGAC,CATTGCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725437,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296981,0,6050STDY14355645,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),19, +5,69725438,6050STDY14355646,,TTGGGTGA,ATAAAGCG,,Duplex-Seq,TTGGGTGA,ATAAAGCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725438,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296982,0,6050STDY14355646,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),20, +5,69725439,6050STDY14355647,,GTTCAAAG,TGCATAAA,,Duplex-Seq,GTTCAAAG,TGCATAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725439,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296983,0,6050STDY14355647,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),21, +5,69725440,6050STDY14355648,,TTAACTTA,GTCATCCT,,Duplex-Seq,TTAACTTA,GTCATCCT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725440,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296984,0,6050STDY14355648,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),22, +5,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004577,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +6,69725419,6050STDY14355627,,CGGAGACA,ATGCGACT,,Duplex-Seq,CGGAGACA,ATGCGACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725419,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296963,0,6050STDY14355627,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +6,69725420,6050STDY14355628,,GTTAACGT,TCACAAAC,,Duplex-Seq,GTTAACGT,TCACAAAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725420,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296964,0,6050STDY14355628,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +6,69725421,6050STDY14355629,,CATTTATT,AGGAGAAA,,Duplex-Seq,CATTTATT,AGGAGAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725421,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296965,0,6050STDY14355629,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +6,69725422,6050STDY14355630,,TTAGCGCA,TCGGCAAA,,Duplex-Seq,TTAGCGCA,TCGGCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725422,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296966,0,6050STDY14355630,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +6,69725423,6050STDY14355631,,TATTCGTA,CTGAAAGA,,Duplex-Seq,TATTCGTA,CTGAAAGA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725423,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296967,0,6050STDY14355631,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_Matched,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +6,69725424,6050STDY14355632,,CTAACTAG,GAAAGGTA,,Duplex-Seq,CTAACTAG,GAAAGGTA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725424,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296968,0,6050STDY14355632,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +6,69725425,6050STDY14355633,,TTTGCAAA,ACACATAT,,Duplex-Seq,TTTGCAAA,ACACATAT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725425,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296969,0,6050STDY14355633,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +6,69725426,6050STDY14355634,,CTTAGAGT,GAACCCTG,,Duplex-Seq,CTTAGAGT,GAACCCTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725426,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296970,0,6050STDY14355634,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +6,69725427,6050STDY14355635,,GGTGGGAA,TAAACCCA,,Duplex-Seq,GGTGGGAA,TAAACCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725427,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296971,0,6050STDY14355635,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +6,69725428,6050STDY14355636,,CCTCCTAA,ATGCACTG,,Duplex-Seq,CCTCCTAA,ATGCACTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725428,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296972,0,6050STDY14355636,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +6,69725429,6050STDY14355637,,TTTCCAGT,ATGCCAAA,,Duplex-Seq,TTTCCAGT,ATGCCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725429,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296973,0,6050STDY14355637,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),11, +6,69725430,6050STDY14355638,,GATATGTG,CCTACTAA,,Duplex-Seq,GATATGTG,CCTACTAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725430,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296974,0,6050STDY14355638,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),12, +6,69725431,6050STDY14355639,,CATGAATC,ATAAACTT,,Duplex-Seq,CATGAATC,ATAAACTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725431,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296975,0,6050STDY14355639,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),13, +6,69725432,6050STDY14355640,,AGTAGTAG,AGGCCGTT,,Duplex-Seq,AGTAGTAG,AGGCCGTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725432,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296976,0,6050STDY14355640,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),14, +6,69725433,6050STDY14355641,,GAGGGCCG,ACCCTCCA,,Duplex-Seq,GAGGGCCG,ACCCTCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725433,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296977,0,6050STDY14355641,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),15, +6,69725434,6050STDY14355642,,TTGTCCAA,CGGATCCC,,Duplex-Seq,TTGTCCAA,CGGATCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725434,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296978,0,6050STDY14355642,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),16, +6,69725435,6050STDY14355643,,CGCAACTG,TGCCATCC,,Duplex-Seq,CGCAACTG,TGCCATCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725435,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296979,0,6050STDY14355643,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),17, +6,69725436,6050STDY14355644,,CATATTCT,CGGACAAG,,Duplex-Seq,CATATTCT,CGGACAAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725436,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296980,0,6050STDY14355644,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_Macthed,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),18, +6,69725437,6050STDY14355645,,GCGGAGAC,CATTGCAC,,Duplex-Seq,GCGGAGAC,CATTGCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725437,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296981,0,6050STDY14355645,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),19, +6,69725438,6050STDY14355646,,TTGGGTGA,ATAAAGCG,,Duplex-Seq,TTGGGTGA,ATAAAGCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725438,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296982,0,6050STDY14355646,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),20, +6,69725439,6050STDY14355647,,GTTCAAAG,TGCATAAA,,Duplex-Seq,GTTCAAAG,TGCATAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725439,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296983,0,6050STDY14355647,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),21, +6,69725440,6050STDY14355648,,TTAACTTA,GTCATCCT,,Duplex-Seq,TTAACTTA,GTCATCCT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725440,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296984,0,6050STDY14355648,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),22, +6,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004578,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +7,69510840,EGAN00001321692,,CCGCGGTT,AGCGCTAG,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGCGGTT,AGCGCTAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510840,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321692,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5407888,1497836,,DDD_MAIN5407888,,,DDD_1_FR00569506,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,1, +7,69510852,EGAN00002042187,,TTATAACC,GATATCGA,Twist_Human_Core_Exome_BI,Twist Pulldown,TTATAACC,GATATCGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510852,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042187,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5710659,1823623,,DDD_MAIN5710659,,,DDD_1_FR00569278,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,2, +7,69510864,EGAN00001298465,,GGACTTGG,CGCAGACG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGACTTGG,CGCAGACG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510864,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298465,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5867091,2001421,,DDD_MAIN5867091,,,DDD_1_D500PK129595,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,3, +7,69510876,EGAN00001300772,,AAGTCCAA,TATGAGTA,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGTCCAA,TATGAGTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510876,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300772,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908944,2050909,,DDD_MAIN5908944,,,DDD_1_D500PK129441,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,4, +7,69510888,EGAN00001300773,,ATCCACTG,AGGTGCGT,Twist_Human_Core_Exome_BI,Twist Pulldown,ATCCACTG,AGGTGCGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510888,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300773,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908952,2050917,,DDD_MAIN5908952,,,DDD_1_D500PK129440,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,5, +7,69510900,EGAN00001301174,,GCTTGTCA,GAACATAC,Twist_Human_Core_Exome_BI,Twist Pulldown,GCTTGTCA,GAACATAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510900,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001301174,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5966748,2115694,,DDD_MAIN5966748,,,DDD_1_D500PK128034,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,6, +7,69510924,EGAN00001304327,,TGGATCGA,GTGCGATA,Twist_Human_Core_Exome_BI,Twist Pulldown,TGGATCGA,GTGCGATA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510924,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304327,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6029045,2203893,,DDD_MAIN6029045,,,DDD_1_D0RG141038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,7, +7,69510889,EGAN00001293788,,CCAAGTCT,AAGGATGA,Twist_Human_Core_Exome_BI,Twist Pulldown,CCAAGTCT,AAGGATGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510889,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293788,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5678531,1788223,,DDD_MAIN5678531,,,DDD_1_D575PK144581,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,8, +7,69510901,EGAN00001304217,,TTGGACTC,GGAAGCAG,Twist_Human_Core_Exome_BI,Twist Pulldown,TTGGACTC,GGAAGCAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510901,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304217,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6028474,2203237,,DDD_MAIN6028474,,,DDD_1_FR03967352,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,9, +7,69510913,EGAN00001293786,,GGCTTAAG,TCGTGACC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCTTAAG,TCGTGACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510913,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293786,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670657,1779062,,DDD_MAIN5670657,,,DDD_1_D500PK132121,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,10, +7,69510925,EGAN00001293787,,AATCCGGA,CTACAGTT,Twist_Human_Core_Exome_BI,Twist Pulldown,AATCCGGA,CTACAGTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510925,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293787,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670663,1779068,,DDD_MAIN5670663,,,DDD_1_D500PK132132,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,11, +7,69510842,EGAN00001321167,,TAATACAG,ATATTCAC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAATACAG,ATATTCAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510842,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321167,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5426807,1517975,,DDD_MAIN5426807,,,DDD_1_FR00569436,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,12, +7,69510854,EGAN00002042190,,CGGCGTGA,GCGCCTGT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGCGTGA,GCGCCTGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510854,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042190,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5714029,1828207,,DDD_MAIN5714029,,,DDD_1_FR00559472,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,13, +7,69510866,EGAN00001298517,,ATGTAAGT,ACTCTATG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGTAAGT,ACTCTATG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510866,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298517,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908825,2050790,,DDD_MAIN5908825,,,DDD_1_D575NB050268,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,14, +7,69510878,EGAN00003580492,,GCACGGAC,GTCTCGCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCACGGAC,GTCTCGCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510878,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580492,,Homo Sapiens,0,,,6278STDY12901037,8350874,0,6278STDY12901037,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0086,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,15, +7,69510890,EGAN00003580498,,GGTACCTT,AAGACGTC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGTACCTT,AAGACGTC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510890,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580498,,Homo Sapiens,0,,,6278STDY12901046,8350881,0,6278STDY12901046,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0025,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,16, +7,69510902,EGAN00003580503,,AACGTTCC,GGAGTACT,Twist_Human_Core_Exome_BI,Twist Pulldown,AACGTTCC,GGAGTACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510902,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580503,,Homo Sapiens,0,,,6278STDY12901051,8350885,0,6278STDY12901051,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0529,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,17, +7,69510914,EGAN00003580513,,GCAGAATT,ACCGGCCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCAGAATT,ACCGGCCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510914,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580513,,Homo Sapiens,0,,,6278STDY12901061,8350893,0,6278STDY12901061,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5040,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,18, +7,69510926,EGAN00003580516,,ATGAGGCC,GTTAATTG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGAGGCC,GTTAATTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510926,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580516,,Homo Sapiens,0,,,6278STDY12901069,8350899,0,6278STDY12901069,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5014,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,19, +7,69510843,EGAN00003580522,,ACTAAGAT,AACCGCGG,Twist_Human_Core_Exome_BI,Twist Pulldown,ACTAAGAT,AACCGCGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510843,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580522,,Homo Sapiens,0,,,6278STDY12901078,8350904,0,6278STDY12901078,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5031,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,20, +7,69510855,EGAN00003580559,,GTCGGAGC,GGTTATAA,Twist_Human_Core_Exome_BI,Twist Pulldown,GTCGGAGC,GGTTATAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510855,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580559,,Homo Sapiens,0,,,6278STDY12901100,8350921,0,6278STDY12901100,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_1550,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,21, +7,69510867,EGAN00003580560,,CTTGGTAT,CCAAGTCC,Twist_Human_Core_Exome_BI,Twist Pulldown,CTTGGTAT,CCAAGTCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510867,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580560,,Homo Sapiens,0,,,6278STDY12901101,8350922,0,6278STDY12901101,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,22, +7,69510879,EGAN00003581911,,TCCAACGC,TTGGACTT,Twist_Human_Core_Exome_BI,Twist Pulldown,TCCAACGC,TTGGACTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510879,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581911,,Homo Sapiens,0,,,6278STDY12902768,8352273,0,6278STDY12902768,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0346,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,23, +7,69510891,EGAN00003581913,,CCGTGAAG,CAGTGGAT,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGTGAAG,CAGTGGAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510891,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581913,,Homo Sapiens,0,,,6278STDY12902770,8352275,0,6278STDY12902770,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0324,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,24, +7,69510903,EGAN00003581920,,TTACAGGA,TGACAAGC,Twist_Human_Core_Exome_BI,Twist Pulldown,TTACAGGA,TGACAAGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510903,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581920,,Homo Sapiens,0,,,6278STDY12902777,8352282,0,6278STDY12902777,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0335,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,25, +7,69510915,EGAN00003581923,,GGCATTCT,CTAGCTTG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCATTCT,CTAGCTTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510915,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581923,,Homo Sapiens,0,,,6278STDY12902780,8352285,0,6278STDY12902780,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0301,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,26, +7,69510844,EGAN00003581941,,TACCGAGG,CCTGAACT,Twist_Human_Core_Exome_BI,Twist Pulldown,TACCGAGG,CCTGAACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510844,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581941,,Homo Sapiens,0,,,6278STDY12902798,8352303,0,6278STDY12902798,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0398,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,27, +7,69510868,EGAN00003581945,,AGCCTCAT,AGTAGAGA,Twist_Human_Core_Exome_BI,Twist Pulldown,AGCCTCAT,AGTAGAGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510868,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581945,,Homo Sapiens,0,,,6278STDY12902802,8352307,0,6278STDY12902802,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0383,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,28, +7,69510880,EGAN00003581946,,GATTCTGC,GACGAGAG,Twist_Human_Core_Exome_BI,Twist Pulldown,GATTCTGC,GACGAGAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510880,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581946,,Homo Sapiens,0,,,6278STDY12902803,8352308,0,6278STDY12902803,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0372,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,29, +7,69510892,EGAN00003581951,,TCGTAGTG,AGACTTGG,Twist_Human_Core_Exome_BI,Twist Pulldown,TCGTAGTG,AGACTTGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510892,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581951,,Homo Sapiens,0,,,6278STDY12902808,8352313,0,6278STDY12902808,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0395,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,30, +7,69510904,EGAN00003581955,,CTACGACA,GAGTCCAA,Twist_Human_Core_Exome_BI,Twist Pulldown,CTACGACA,GAGTCCAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510904,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581955,,Homo Sapiens,0,,,6278STDY12902811,8352316,0,6278STDY12902811,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0362,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,31, +7,69510916,EGAN00003581958,,TAAGTGGT,CTTAAGCC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAAGTGGT,CTTAAGCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510916,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581958,,Homo Sapiens,0,,,6278STDY12902815,8352320,0,6278STDY12902815,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0396,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,32, +7,69510928,EGAN00003581970,,CGGACAAC,TCCGGATT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGACAAC,TCCGGATT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510928,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581970,,Homo Sapiens,0,,,6278STDY12902827,8352332,0,6278STDY12902827,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0332,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,33, +7,69510845,EGAN00003581974,,ATATGGAT,CTGTATTA,Twist_Human_Core_Exome_BI,Twist Pulldown,ATATGGAT,CTGTATTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510845,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581974,,Homo Sapiens,0,,,6278STDY12902831,8352336,0,6278STDY12902831,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0376,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,34, +7,69510857,EGAN00003581980,,GCGCAAGC,TCACGCCG,Twist_Human_Core_Exome_BI,Twist Pulldown,GCGCAAGC,TCACGCCG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510857,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581980,,Homo Sapiens,0,,,6278STDY12902837,8352342,0,6278STDY12902837,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0379,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,35, +7,69510869,EGAN00003581983,,AAGATACT,ACTTACAT,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGATACT,ACTTACAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510869,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581983,,Homo Sapiens,0,,,6278STDY12902840,8352345,0,6278STDY12902840,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0355,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,36, +7,69510881,EGAN00003581988,,GGAGCGTC,GTCCGTGC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGAGCGTC,GTCCGTGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510881,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581988,,Homo Sapiens,0,,,6278STDY12902845,8352350,0,6278STDY12902845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0361,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,37, +7,69510893,EGAN00003582081,,ATGGCATG,AAGGTACC,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGGCATG,AAGGTACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510893,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003582081,,Homo Sapiens,0,,,6278STDY12902847,8352352,0,6278STDY12902847,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0368,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,38, +7,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004572,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +8,69510840,EGAN00001321692,,CCGCGGTT,AGCGCTAG,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGCGGTT,AGCGCTAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510840,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321692,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5407888,1497836,,DDD_MAIN5407888,,,DDD_1_FR00569506,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,1, +8,69510852,EGAN00002042187,,TTATAACC,GATATCGA,Twist_Human_Core_Exome_BI,Twist Pulldown,TTATAACC,GATATCGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510852,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042187,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5710659,1823623,,DDD_MAIN5710659,,,DDD_1_FR00569278,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,2, +8,69510864,EGAN00001298465,,GGACTTGG,CGCAGACG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGACTTGG,CGCAGACG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510864,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298465,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5867091,2001421,,DDD_MAIN5867091,,,DDD_1_D500PK129595,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,3, +8,69510876,EGAN00001300772,,AAGTCCAA,TATGAGTA,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGTCCAA,TATGAGTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510876,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300772,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908944,2050909,,DDD_MAIN5908944,,,DDD_1_D500PK129441,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,4, +8,69510888,EGAN00001300773,,ATCCACTG,AGGTGCGT,Twist_Human_Core_Exome_BI,Twist Pulldown,ATCCACTG,AGGTGCGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510888,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300773,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908952,2050917,,DDD_MAIN5908952,,,DDD_1_D500PK129440,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,5, +8,69510900,EGAN00001301174,,GCTTGTCA,GAACATAC,Twist_Human_Core_Exome_BI,Twist Pulldown,GCTTGTCA,GAACATAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510900,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001301174,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5966748,2115694,,DDD_MAIN5966748,,,DDD_1_D500PK128034,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,6, +8,69510924,EGAN00001304327,,TGGATCGA,GTGCGATA,Twist_Human_Core_Exome_BI,Twist Pulldown,TGGATCGA,GTGCGATA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510924,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304327,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6029045,2203893,,DDD_MAIN6029045,,,DDD_1_D0RG141038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,7, +8,69510889,EGAN00001293788,,CCAAGTCT,AAGGATGA,Twist_Human_Core_Exome_BI,Twist Pulldown,CCAAGTCT,AAGGATGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510889,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293788,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5678531,1788223,,DDD_MAIN5678531,,,DDD_1_D575PK144581,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,8, +8,69510901,EGAN00001304217,,TTGGACTC,GGAAGCAG,Twist_Human_Core_Exome_BI,Twist Pulldown,TTGGACTC,GGAAGCAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510901,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304217,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6028474,2203237,,DDD_MAIN6028474,,,DDD_1_FR03967352,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,9, +8,69510913,EGAN00001293786,,GGCTTAAG,TCGTGACC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCTTAAG,TCGTGACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510913,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293786,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670657,1779062,,DDD_MAIN5670657,,,DDD_1_D500PK132121,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,10, +8,69510925,EGAN00001293787,,AATCCGGA,CTACAGTT,Twist_Human_Core_Exome_BI,Twist Pulldown,AATCCGGA,CTACAGTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510925,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293787,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670663,1779068,,DDD_MAIN5670663,,,DDD_1_D500PK132132,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,11, +8,69510842,EGAN00001321167,,TAATACAG,ATATTCAC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAATACAG,ATATTCAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510842,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321167,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5426807,1517975,,DDD_MAIN5426807,,,DDD_1_FR00569436,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,12, +8,69510854,EGAN00002042190,,CGGCGTGA,GCGCCTGT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGCGTGA,GCGCCTGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510854,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042190,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5714029,1828207,,DDD_MAIN5714029,,,DDD_1_FR00559472,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,13, +8,69510866,EGAN00001298517,,ATGTAAGT,ACTCTATG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGTAAGT,ACTCTATG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510866,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298517,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908825,2050790,,DDD_MAIN5908825,,,DDD_1_D575NB050268,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,14, +8,69510878,EGAN00003580492,,GCACGGAC,GTCTCGCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCACGGAC,GTCTCGCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510878,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580492,,Homo Sapiens,0,,,6278STDY12901037,8350874,0,6278STDY12901037,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0086,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,15, +8,69510890,EGAN00003580498,,GGTACCTT,AAGACGTC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGTACCTT,AAGACGTC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510890,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580498,,Homo Sapiens,0,,,6278STDY12901046,8350881,0,6278STDY12901046,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0025,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,16, +8,69510902,EGAN00003580503,,AACGTTCC,GGAGTACT,Twist_Human_Core_Exome_BI,Twist Pulldown,AACGTTCC,GGAGTACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510902,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580503,,Homo Sapiens,0,,,6278STDY12901051,8350885,0,6278STDY12901051,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0529,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,17, +8,69510914,EGAN00003580513,,GCAGAATT,ACCGGCCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCAGAATT,ACCGGCCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510914,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580513,,Homo Sapiens,0,,,6278STDY12901061,8350893,0,6278STDY12901061,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5040,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,18, +8,69510926,EGAN00003580516,,ATGAGGCC,GTTAATTG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGAGGCC,GTTAATTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510926,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580516,,Homo Sapiens,0,,,6278STDY12901069,8350899,0,6278STDY12901069,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5014,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,19, +8,69510843,EGAN00003580522,,ACTAAGAT,AACCGCGG,Twist_Human_Core_Exome_BI,Twist Pulldown,ACTAAGAT,AACCGCGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510843,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580522,,Homo Sapiens,0,,,6278STDY12901078,8350904,0,6278STDY12901078,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5031,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,20, +8,69510855,EGAN00003580559,,GTCGGAGC,GGTTATAA,Twist_Human_Core_Exome_BI,Twist Pulldown,GTCGGAGC,GGTTATAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510855,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580559,,Homo Sapiens,0,,,6278STDY12901100,8350921,0,6278STDY12901100,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_1550,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,21, +8,69510867,EGAN00003580560,,CTTGGTAT,CCAAGTCC,Twist_Human_Core_Exome_BI,Twist Pulldown,CTTGGTAT,CCAAGTCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510867,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580560,,Homo Sapiens,0,,,6278STDY12901101,8350922,0,6278STDY12901101,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,22, +8,69510879,EGAN00003581911,,TCCAACGC,TTGGACTT,Twist_Human_Core_Exome_BI,Twist Pulldown,TCCAACGC,TTGGACTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510879,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581911,,Homo Sapiens,0,,,6278STDY12902768,8352273,0,6278STDY12902768,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0346,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,23, +8,69510891,EGAN00003581913,,CCGTGAAG,CAGTGGAT,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGTGAAG,CAGTGGAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510891,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581913,,Homo Sapiens,0,,,6278STDY12902770,8352275,0,6278STDY12902770,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0324,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,24, +8,69510903,EGAN00003581920,,TTACAGGA,TGACAAGC,Twist_Human_Core_Exome_BI,Twist Pulldown,TTACAGGA,TGACAAGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510903,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581920,,Homo Sapiens,0,,,6278STDY12902777,8352282,0,6278STDY12902777,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0335,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,25, +8,69510915,EGAN00003581923,,GGCATTCT,CTAGCTTG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCATTCT,CTAGCTTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510915,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581923,,Homo Sapiens,0,,,6278STDY12902780,8352285,0,6278STDY12902780,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0301,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,26, +8,69510844,EGAN00003581941,,TACCGAGG,CCTGAACT,Twist_Human_Core_Exome_BI,Twist Pulldown,TACCGAGG,CCTGAACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510844,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581941,,Homo Sapiens,0,,,6278STDY12902798,8352303,0,6278STDY12902798,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0398,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,27, +8,69510868,EGAN00003581945,,AGCCTCAT,AGTAGAGA,Twist_Human_Core_Exome_BI,Twist Pulldown,AGCCTCAT,AGTAGAGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510868,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581945,,Homo Sapiens,0,,,6278STDY12902802,8352307,0,6278STDY12902802,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0383,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,28, +8,69510880,EGAN00003581946,,GATTCTGC,GACGAGAG,Twist_Human_Core_Exome_BI,Twist Pulldown,GATTCTGC,GACGAGAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510880,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581946,,Homo Sapiens,0,,,6278STDY12902803,8352308,0,6278STDY12902803,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0372,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,29, +8,69510892,EGAN00003581951,,TCGTAGTG,AGACTTGG,Twist_Human_Core_Exome_BI,Twist Pulldown,TCGTAGTG,AGACTTGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510892,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581951,,Homo Sapiens,0,,,6278STDY12902808,8352313,0,6278STDY12902808,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0395,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,30, +8,69510904,EGAN00003581955,,CTACGACA,GAGTCCAA,Twist_Human_Core_Exome_BI,Twist Pulldown,CTACGACA,GAGTCCAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510904,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581955,,Homo Sapiens,0,,,6278STDY12902811,8352316,0,6278STDY12902811,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0362,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,31, +8,69510916,EGAN00003581958,,TAAGTGGT,CTTAAGCC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAAGTGGT,CTTAAGCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510916,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581958,,Homo Sapiens,0,,,6278STDY12902815,8352320,0,6278STDY12902815,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0396,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,32, +8,69510928,EGAN00003581970,,CGGACAAC,TCCGGATT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGACAAC,TCCGGATT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510928,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581970,,Homo Sapiens,0,,,6278STDY12902827,8352332,0,6278STDY12902827,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0332,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,33, +8,69510845,EGAN00003581974,,ATATGGAT,CTGTATTA,Twist_Human_Core_Exome_BI,Twist Pulldown,ATATGGAT,CTGTATTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510845,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581974,,Homo Sapiens,0,,,6278STDY12902831,8352336,0,6278STDY12902831,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0376,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,34, +8,69510857,EGAN00003581980,,GCGCAAGC,TCACGCCG,Twist_Human_Core_Exome_BI,Twist Pulldown,GCGCAAGC,TCACGCCG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510857,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581980,,Homo Sapiens,0,,,6278STDY12902837,8352342,0,6278STDY12902837,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0379,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,35, +8,69510869,EGAN00003581983,,AAGATACT,ACTTACAT,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGATACT,ACTTACAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510869,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581983,,Homo Sapiens,0,,,6278STDY12902840,8352345,0,6278STDY12902840,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0355,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,36, +8,69510881,EGAN00003581988,,GGAGCGTC,GTCCGTGC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGAGCGTC,GTCCGTGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510881,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581988,,Homo Sapiens,0,,,6278STDY12902845,8352350,0,6278STDY12902845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0361,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,37, +8,69510893,EGAN00003582081,,ATGGCATG,AAGGTACC,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGGCATG,AAGGTACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510893,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003582081,,Homo Sapiens,0,,,6278STDY12902847,8352352,0,6278STDY12902847,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0368,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,38, +8,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004571,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, From 7a25f377deeae99fd9a2f11ace1b5ae479e7fdd3 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 17 Nov 2023 12:27:52 +0000 Subject: [PATCH 27/35] Distinguish between NovaSeq and NovaSeqX RunParams. We use the name of the Application in RunParameters.xml to detect that the instrument belongs to the NovaSeq type. Newer NovaSeqX instrument we have has the following definition for the application: NovaSeqXSeries Control Software This pull request fixes the reg exp we use to ensure that the above definition does not result in the instrument being classified as NovaSeq. --- MANIFEST | 1 + lib/npg_tracking/illumina/run/long_info.pm | 2 +- t/60-illumina-run-long_info.t | 12 ++- .../RunParameters.novaseqx.prod.xml | 87 +++++++++++++++++++ 4 files changed, 97 insertions(+), 5 deletions(-) create mode 100644 t/data/run_params/RunParameters.novaseqx.prod.xml diff --git a/MANIFEST b/MANIFEST index 346e5a4b..19a00573 100644 --- a/MANIFEST +++ b/MANIFEST @@ -666,6 +666,7 @@ t/data/run_params/runParameters.hiseqx.upgraded.xml t/data/run_params/runParameters.hiseqx.xml t/data/run_params/runParameters.miseq.xml t/data/run_params/RunParameters.novaseq.xp.lite.xml +t/data/run_params/RunParameters.novaseqx.prod.xml t/data/samplesheet/samplesheet_7753.csv t/data/samplesheet/samplesheet_27483.csv t/data/samplesheet/samplesheet_33990.csv diff --git a/lib/npg_tracking/illumina/run/long_info.pm b/lib/npg_tracking/illumina/run/long_info.pm index 5e321dd4..69377a7d 100644 --- a/lib/npg_tracking/illumina/run/long_info.pm +++ b/lib/npg_tracking/illumina/run/long_info.pm @@ -592,7 +592,7 @@ instrument belonging to NovaSeq platform. sub platform_NovaSeq { my $self = shift; - return $self->_software_application_name() =~ /NovaSeq/xms; + return $self->_software_application_name() =~ /NovaSeq(?!X)/xms; } =head2 platform_NovaSeqX diff --git a/t/60-illumina-run-long_info.t b/t/60-illumina-run-long_info.t index 5015437a..7ae660c8 100644 --- a/t/60-illumina-run-long_info.t +++ b/t/60-illumina-run-long_info.t @@ -29,7 +29,7 @@ package main; my $basedir = tempdir( CLEANUP => 1 ); subtest 'retrieving information from runParameters.xml' => sub { - plan tests => 167; + plan tests => 177; my $rf = join q[/], $basedir, 'runfolder'; mkdir $rf; @@ -52,7 +52,8 @@ subtest 'retrieving information from runParameters.xml' => sub { RunParameters.novaseq.xp.xml RunParameters.novaseq.xp.v1.5.xml runParameters.hiseq.rr.truseq.xml - RunParameters.novaseqx.xml + RunParameters.novaseqx.xml + RunParameters.novaseqx.prod.xml /; my $dir = 't/data/run_params'; @@ -117,8 +118,11 @@ subtest 'retrieving information from runParameters.xml' => sub { } else { ok (!$li->uses_patterned_flowcell, 'not patterned flowcell'); } - - ok (!$li->onboard_analysis_planned(), 'onboard analysis is not planned'); + if ($f =~ /novaseqx\.prod/) { + ok ($li->onboard_analysis_planned(), 'onboard analysis is planned'); + } else { + ok (!$li->onboard_analysis_planned(), 'onboard analysis is not planned'); + } unlink $name; } diff --git a/t/data/run_params/RunParameters.novaseqx.prod.xml b/t/data/run_params/RunParameters.novaseqx.prod.xml new file mode 100644 index 00000000..bd9c75b5 --- /dev/null +++ b/t/data/run_params/RunParameters.novaseqx.prod.xml @@ -0,0 +1,87 @@ + + + B + NovaSeqXSeries Control Software + 1.2.0.26276 + //nx2-esa.dnapipelines.sanger.ac.uk/staging/IL_seq_data/incoming/20231019_LH00275_0006_B19NJCA4LE + InstrumentPerformance + LocalOrchestrated + LocalAnalysis + NovaSeqXPlus + LH00275 + 20231019_LH00275_0006_B19NJCA4LE + 6 + 25B Sequencing + 25B-01.02.00 + 47999_NX2_B + NovaSeqXSeries B4 + NovaSeqXSeriesB4 + + + 19NJCA4LE + 9345L1E1 + 20088038 + 2024-04-29T00:00:00+01:00 + FlowCell + 4 + 1.0 + 25B + + + LC2305090085-1 + 23050901 + 20089853 + 2024-08-09T00:00:00+01:00 + Buffer + 3 + 1.0 + Universal + + + LC1001941-LS1 + 1000018698 + 20101913 + 2025-08-25T00:00:00+01:00 + SampleTube + 3 + 1.0 + 8 Lane + + + LC4044182-25B3 + 20784608 + 20066626 + 2024-08-20T00:00:00+01:00 + Reagent + 4 + 1.5 + 25B 300c + + + LC2000520-LI5 + 17792769 + 20090674 + 2024-05-11T00:00:00+01:00 + Lyo + 11 + 1.5 + High + + + + + + + + + + + 4.1.7 + + DRAGEN BCL Convert + DRAGEN Germline + + + + false + \ No newline at end of file From 1bdc2796eca0fd315c5c1a23976d33ffefedc333 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Fri, 17 Nov 2023 14:04:55 +0000 Subject: [PATCH 28/35] More robust evaluation. --- lib/npg_tracking/illumina/run/long_info.pm | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/lib/npg_tracking/illumina/run/long_info.pm b/lib/npg_tracking/illumina/run/long_info.pm index 69377a7d..3e22c310 100644 --- a/lib/npg_tracking/illumina/run/long_info.pm +++ b/lib/npg_tracking/illumina/run/long_info.pm @@ -592,7 +592,8 @@ instrument belonging to NovaSeq platform. sub platform_NovaSeq { my $self = shift; - return $self->_software_application_name() =~ /NovaSeq(?!X)/xms; + return (!$self->platform_NovaSeqX() && + ($self->_software_application_name() =~ /NovaSeq[ ]/xms)); } =head2 platform_NovaSeqX From b6bfc157c5f662aabfce58d7236f499f33c2bfa7 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 22 Nov 2023 16:15:01 +0000 Subject: [PATCH 29/35] Added a NovaSeqX samplesheet --- t/data/samplesheet/samplesheet_47995.csv | 184 +++++++++++++++++++++++ 1 file changed, 184 insertions(+) create mode 100644 t/data/samplesheet/samplesheet_47995.csv diff --git a/t/data/samplesheet/samplesheet_47995.csv b/t/data/samplesheet/samplesheet_47995.csv new file mode 100644 index 00000000..e9b16751 --- /dev/null +++ b/t/data/samplesheet/samplesheet_47995.csv @@ -0,0 +1,184 @@ +[Data],,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, +Lane,Sample_ID,Sample_Name,GenomeFolder,Index,Index2,bait_name,default_library_type,default_tag_sequence,default_tagtwo_sequence,email_addresses,email_addresses_of_followers,email_addresses_of_managers,email_addresses_of_owners,gbs_plex_name,is_control,is_pool,lane_id,lane_priority,library_name,organism,organism_taxon_id,project_cost_code,project_id,project_name,purpose,qc_state,request_id,required_insert_size_range,sample_accession_number,sample_cohort,sample_common_name,sample_consent_withdrawn,sample_control_type,sample_description,sample_donor_id,sample_id,sample_is_control,sample_name,sample_public_name,sample_reference_genome,sample_supplier_name,spiked_phix_tag_index,study_accession_number,study_alignments_in_bam,study_contains_nonconsented_human,study_contains_nonconsented_xahuman,study_description,study_id,study_name,study_reference_genome,study_separate_y_chromosome_data,study_title,tag_index, +1,65934716,EGAN00004177411,,CCTTCTCT,ATTGAGAG,TE-95148282,Targeted NanoSeq Pulldown Twist,CCTTCTCT,ATTGAGAG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934716,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177411,Normal,Homo sapiens,0,,,PD45703b_tds0003,8508809,0,6751STDY13219549,PD45703b_tds0003,,PD45703b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,1, +1,65934633,EGAN00004177412,,TTTGAGGG,CCCAATCA,TE-95148282,Targeted NanoSeq Pulldown Twist,TTTGAGGG,CCCAATCA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934633,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177412,Normal,Homo sapiens,0,,,PD45704b_tds0002,8508810,0,6751STDY13219550,PD45704b_tds0002,,PD45704b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,2, +1,65934645,EGAN00004177418,,GGCCTGGC,TTGCAATC,TE-95148282,Targeted NanoSeq Pulldown Twist,GGCCTGGC,TTGCAATC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934645,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177418,Normal,Homo sapiens,0,,,PD45704b_tds0003,8508815,0,6751STDY13219555,PD45704b_tds0003,,PD45704b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,3, +1,65934657,EGAN00004177402,,AAAGTGAA,ATGGCAGC,TE-95148282,Targeted NanoSeq Pulldown Twist,AAAGTGAA,ATGGCAGC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934657,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177402,Normal,Homo sapiens,0,,,PD43959b_tds0002,8508801,0,6751STDY13219541,PD43959b_tds0002,,PD43959b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,4, +1,65934669,EGAN00004177414,,ACTCGAAA,CACGCGAC,TE-95148282,Targeted NanoSeq Pulldown Twist,ACTCGAAA,CACGCGAC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934669,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177414,Normal,Homo sapiens,0,,,PD45707b_tds0002,8508812,0,6751STDY13219552,PD45707b_tds0002,,PD45707b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,5, +1,65934681,EGAN00004177417,,CGATTGCA,ACCCAGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,CGATTGCA,ACCCAGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934681,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177417,Normal,Homo sapiens,0,,,PD49159b_tds0002,8508816,0,6751STDY13219556,PD49159b_tds0002,,PD49159b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,6, +1,65934693,EGAN00004177419,,GTAAGCGA,GTTTGGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTAAGCGA,GTTTGGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934693,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177419,Normal,Homo sapiens,0,,,PD49134b_tds0002,8508817,0,6751STDY13219557,PD49134b_tds0002,,PD49134b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,7, +1,65934705,EGAN00004177400,,TTCTTCAG,ACCACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,TTCTTCAG,ACCACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934705,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177400,Normal,Homo sapiens,0,,,PD43957b_tds0002,8508799,0,6751STDY13219539,PD43957b_tds0002,,PD43957b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,8, +1,65934717,EGAN00004177407,,CGTGGATA,TTCCGGTG,TE-95148282,Targeted NanoSeq Pulldown Twist,CGTGGATA,TTCCGGTG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934717,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177407,Normal,Homo sapiens,0,,,PD43958b_tds0002,8508800,0,6751STDY13219540,PD43958b_tds0002,,PD43958b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,9, +1,65934634,EGAN00004177403,,CACTTTGC,AGTCGATG,TE-95148282,Targeted NanoSeq Pulldown Twist,CACTTTGC,AGTCGATG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934634,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177403,Normal,Homo sapiens,0,,,PD43960b_tds0002,8508802,0,6751STDY13219542,PD43960b_tds0002,,PD43960b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,10, +1,65934646,EGAN00004177404,,GTGTCGGT,GATGCGTC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGTCGGT,GATGCGTC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934646,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177404,Normal,Homo sapiens,0,,,PD43961b_tds0002,8508803,0,6751STDY13219543,PD43961b_tds0002,,PD43961b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,11, +1,65934658,EGAN00004177405,,ACGTAACA,ACATTCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,ACGTAACA,ACATTCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934658,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177405,Normal,Homo sapiens,0,,,PD43962b_tds0003,8508804,0,6751STDY13219544,PD43962b_tds0003,,PD43962b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,12, +1,65934670,EGAN00004177406,,CTTTCGAC,CAGACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,CTTTCGAC,CAGACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934670,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177406,Normal,Homo sapiens,0,,,PD43964b_tds0002,8508805,0,6751STDY13219545,PD43964b_tds0002,,PD43964b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,13, +1,65934682,EGAN00004177410,,GTGACCTA,ATAGCGTT,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGACCTA,ATAGCGTT,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934682,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177410,Normal,Homo sapiens,0,,,PD43965b_tds0002,8508806,0,6751STDY13219546,PD43965b_tds0002,,PD43965b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,14, +1,65934694,EGAN00004177408,,GTCCTAAC,TACGCCGA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTCCTAAC,TACGCCGA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934694,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177408,Normal,Homo sapiens,0,,,PD45701b_tds0002,8508807,0,6751STDY13219547,PD45701b_tds0002,,PD45701b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,15, +1,65934706,EGAN00004177413,,GTGCAGGG,AGTCTGCC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGCAGGG,AGTCTGCC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934706,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177413,Normal,Homo sapiens,0,,,PD45705b_tds0002,8508811,0,6751STDY13219551,PD45705b_tds0002,,PD45705b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,16, +1,65934718,EGAN00004177416,,TGCGGTGT,GCAACCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,TGCGGTGT,GCAACCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004573,0,65934718,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177416,Normal,Homo sapiens,0,,,PD49155b_tds0002,8508814,0,6751STDY13219554,PD49155b_tds0002,,PD49155b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,17, +1,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004573,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +2,65934716,EGAN00004177411,,CCTTCTCT,ATTGAGAG,TE-95148282,Targeted NanoSeq Pulldown Twist,CCTTCTCT,ATTGAGAG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934716,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177411,Normal,Homo sapiens,0,,,PD45703b_tds0003,8508809,0,6751STDY13219549,PD45703b_tds0003,,PD45703b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,1, +2,65934633,EGAN00004177412,,TTTGAGGG,CCCAATCA,TE-95148282,Targeted NanoSeq Pulldown Twist,TTTGAGGG,CCCAATCA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934633,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177412,Normal,Homo sapiens,0,,,PD45704b_tds0002,8508810,0,6751STDY13219550,PD45704b_tds0002,,PD45704b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,2, +2,65934645,EGAN00004177418,,GGCCTGGC,TTGCAATC,TE-95148282,Targeted NanoSeq Pulldown Twist,GGCCTGGC,TTGCAATC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934645,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177418,Normal,Homo sapiens,0,,,PD45704b_tds0003,8508815,0,6751STDY13219555,PD45704b_tds0003,,PD45704b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,3, +2,65934657,EGAN00004177402,,AAAGTGAA,ATGGCAGC,TE-95148282,Targeted NanoSeq Pulldown Twist,AAAGTGAA,ATGGCAGC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934657,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177402,Normal,Homo sapiens,0,,,PD43959b_tds0002,8508801,0,6751STDY13219541,PD43959b_tds0002,,PD43959b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,4, +2,65934669,EGAN00004177414,,ACTCGAAA,CACGCGAC,TE-95148282,Targeted NanoSeq Pulldown Twist,ACTCGAAA,CACGCGAC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934669,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177414,Normal,Homo sapiens,0,,,PD45707b_tds0002,8508812,0,6751STDY13219552,PD45707b_tds0002,,PD45707b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,5, +2,65934681,EGAN00004177417,,CGATTGCA,ACCCAGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,CGATTGCA,ACCCAGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934681,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177417,Normal,Homo sapiens,0,,,PD49159b_tds0002,8508816,0,6751STDY13219556,PD49159b_tds0002,,PD49159b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,6, +2,65934693,EGAN00004177419,,GTAAGCGA,GTTTGGAA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTAAGCGA,GTTTGGAA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934693,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177419,Normal,Homo sapiens,0,,,PD49134b_tds0002,8508817,0,6751STDY13219557,PD49134b_tds0002,,PD49134b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,7, +2,65934705,EGAN00004177400,,TTCTTCAG,ACCACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,TTCTTCAG,ACCACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934705,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177400,Normal,Homo sapiens,0,,,PD43957b_tds0002,8508799,0,6751STDY13219539,PD43957b_tds0002,,PD43957b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,8, +2,65934717,EGAN00004177407,,CGTGGATA,TTCCGGTG,TE-95148282,Targeted NanoSeq Pulldown Twist,CGTGGATA,TTCCGGTG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934717,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177407,Normal,Homo sapiens,0,,,PD43958b_tds0002,8508800,0,6751STDY13219540,PD43958b_tds0002,,PD43958b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,9, +2,65934634,EGAN00004177403,,CACTTTGC,AGTCGATG,TE-95148282,Targeted NanoSeq Pulldown Twist,CACTTTGC,AGTCGATG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934634,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177403,Normal,Homo sapiens,0,,,PD43960b_tds0002,8508802,0,6751STDY13219542,PD43960b_tds0002,,PD43960b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,10, +2,65934646,EGAN00004177404,,GTGTCGGT,GATGCGTC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGTCGGT,GATGCGTC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934646,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177404,Normal,Homo sapiens,0,,,PD43961b_tds0002,8508803,0,6751STDY13219543,PD43961b_tds0002,,PD43961b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,11, +2,65934658,EGAN00004177405,,ACGTAACA,ACATTCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,ACGTAACA,ACATTCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934658,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177405,Normal,Homo sapiens,0,,,PD43962b_tds0003,8508804,0,6751STDY13219544,PD43962b_tds0003,,PD43962b_tds0003,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,12, +2,65934670,EGAN00004177406,,CTTTCGAC,CAGACTGG,TE-95148282,Targeted NanoSeq Pulldown Twist,CTTTCGAC,CAGACTGG,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934670,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177406,Normal,Homo sapiens,0,,,PD43964b_tds0002,8508805,0,6751STDY13219545,PD43964b_tds0002,,PD43964b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,13, +2,65934682,EGAN00004177410,,GTGACCTA,ATAGCGTT,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGACCTA,ATAGCGTT,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934682,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177410,Normal,Homo sapiens,0,,,PD43965b_tds0002,8508806,0,6751STDY13219546,PD43965b_tds0002,,PD43965b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,14, +2,65934694,EGAN00004177408,,GTCCTAAC,TACGCCGA,TE-95148282,Targeted NanoSeq Pulldown Twist,GTCCTAAC,TACGCCGA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934694,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177408,Normal,Homo sapiens,0,,,PD45701b_tds0002,8508807,0,6751STDY13219547,PD45701b_tds0002,,PD45701b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,15, +2,65934706,EGAN00004177413,,GTGCAGGG,AGTCTGCC,TE-95148282,Targeted NanoSeq Pulldown Twist,GTGCAGGG,AGTCTGCC,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934706,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177413,Normal,Homo sapiens,0,,,PD45705b_tds0002,8508811,0,6751STDY13219551,PD45705b_tds0002,,PD45705b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,16, +2,65934718,EGAN00004177416,,TGCGGTGT,GCAACCTA,TE-95148282,Targeted NanoSeq Pulldown Twist,TGCGGTGT,GCAACCTA,user1@my.com user2@my.com user3@my.com user4@my.com user5@my.com,user1@my.com user1@my.com user4@my.com user4@my.com user5@my.com user5@my.com,user2@my.com user2@my.com user3@my.com user3@my.com , ,,0,0,70004574,0,65934718,,9606,S4360,,,standard,,,from:100 to:400,EGAN00004177416,Normal,Homo sapiens,0,,,PD49155b_tds0002,8508814,0,6751STDY13219554,PD49155b_tds0002,,PD49155b_tds0002,888,EGAS00001005918,1,0,0,Targeted NanoSeq in synoviums from a number of donorsas.,6751,Targeted NanoSeq_Synovium,Homo_sapiens (1000Genomes_hs37d5 %2B ensembl_75_transcriptome),0,Targeted NanoSeq_Synovium,17, +2,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004574,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +3,69723082,6050STDY14354621,,TTGATTCC,AGAAGCCC,,Duplex-Seq,TTGATTCC,AGAAGCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723082,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296053,0,6050STDY14354621,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +3,69723083,6050STDY14354622,,CATCATTT,ACCTAACT,,Duplex-Seq,CATCATTT,ACCTAACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723083,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296054,0,6050STDY14354622,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +3,69723084,6050STDY14354623,,ATATGCGC,GCTAATTG,,Duplex-Seq,ATATGCGC,GCTAATTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723084,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296055,0,6050STDY14354623,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +3,69723085,6050STDY14354624,,GTAAATGC,GGTAGGTG,,Duplex-Seq,GTAAATGC,GGTAGGTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723085,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296056,0,6050STDY14354624,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +3,69723086,6050STDY14354625,,TTAGTAGA,AAATTCAC,,Duplex-Seq,TTAGTAGA,AAATTCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723086,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296057,0,6050STDY14354625,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +3,69723087,6050STDY14354626,,CTGATGCT,CTGGATTT,,Duplex-Seq,CTGATGCT,CTGGATTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723087,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296058,0,6050STDY14354626,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +3,69723088,6050STDY14354627,,CTTGCGTG,TACTGCCG,,Duplex-Seq,CTTGCGTG,TACTGCCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723088,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296059,0,6050STDY14354627,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +3,69723089,6050STDY14354628,,CTGTCACA,CATTTATC,,Duplex-Seq,CTGTCACA,CATTTATC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723089,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296060,0,6050STDY14354628,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +3,69723090,6050STDY14354629,,GCCTAGGG,AGTTGGAG,,Duplex-Seq,GCCTAGGG,AGTTGGAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723090,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296061,0,6050STDY14354629,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +3,69723091,6050STDY14354630,,CTTACTCA,TCTCGACC,,Duplex-Seq,CTTACTCA,TCTCGACC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004575,0,69723091,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296062,0,6050STDY14354630,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +3,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004575,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +4,69723082,6050STDY14354621,,TTGATTCC,AGAAGCCC,,Duplex-Seq,TTGATTCC,AGAAGCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723082,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296053,0,6050STDY14354621,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +4,69723083,6050STDY14354622,,CATCATTT,ACCTAACT,,Duplex-Seq,CATCATTT,ACCTAACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723083,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296054,0,6050STDY14354622,,Homo_sapiens (1000Genomes_hs37d5),ShearingNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +4,69723084,6050STDY14354623,,ATATGCGC,GCTAATTG,,Duplex-Seq,ATATGCGC,GCTAATTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723084,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296055,0,6050STDY14354623,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +4,69723085,6050STDY14354624,,GTAAATGC,GGTAGGTG,,Duplex-Seq,GTAAATGC,GGTAGGTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723085,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296056,0,6050STDY14354624,,Homo_sapiens (1000Genomes_hs37d5),ShearingUltraII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +4,69723086,6050STDY14354625,,TTAGTAGA,AAATTCAC,,Duplex-Seq,TTAGTAGA,AAATTCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723086,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296057,0,6050STDY14354625,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +4,69723087,6050STDY14354626,,CTGATGCT,CTGGATTT,,Duplex-Seq,CTGATGCT,CTGGATTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723087,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296058,0,6050STDY14354626,,Homo_sapiens (1000Genomes_hs37d5),USNanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +4,69723088,6050STDY14354627,,CTTGCGTG,TACTGCCG,,Duplex-Seq,CTTGCGTG,TACTGCCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723088,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296059,0,6050STDY14354627,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +4,69723089,6050STDY14354628,,CTGTCACA,CATTTATC,,Duplex-Seq,CTGTCACA,CATTTATC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723089,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296060,0,6050STDY14354628,,Homo_sapiens (1000Genomes_hs37d5),R1.1NanoSeq_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +4,69723090,6050STDY14354629,,GCCTAGGG,AGTTGGAG,,Duplex-Seq,GCCTAGGG,AGTTGGAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723090,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296061,0,6050STDY14354629,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep1,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +4,69723091,6050STDY14354630,,CTTACTCA,TCTCGACC,,Duplex-Seq,CTTACTCA,TCTCGACC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004576,0,69723091,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD47269g,9296062,0,6050STDY14354630,,Homo_sapiens (1000Genomes_hs37d5),USUII_Rep2,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +4,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004576,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +5,69725419,6050STDY14355627,,CGGAGACA,ATGCGACT,,Duplex-Seq,CGGAGACA,ATGCGACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725419,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296963,0,6050STDY14355627,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +5,69725420,6050STDY14355628,,GTTAACGT,TCACAAAC,,Duplex-Seq,GTTAACGT,TCACAAAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725420,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296964,0,6050STDY14355628,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +5,69725421,6050STDY14355629,,CATTTATT,AGGAGAAA,,Duplex-Seq,CATTTATT,AGGAGAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725421,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296965,0,6050STDY14355629,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +5,69725422,6050STDY14355630,,TTAGCGCA,TCGGCAAA,,Duplex-Seq,TTAGCGCA,TCGGCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725422,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296966,0,6050STDY14355630,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +5,69725423,6050STDY14355631,,TATTCGTA,CTGAAAGA,,Duplex-Seq,TATTCGTA,CTGAAAGA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725423,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296967,0,6050STDY14355631,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_Matched,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +5,69725424,6050STDY14355632,,CTAACTAG,GAAAGGTA,,Duplex-Seq,CTAACTAG,GAAAGGTA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725424,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296968,0,6050STDY14355632,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +5,69725425,6050STDY14355633,,TTTGCAAA,ACACATAT,,Duplex-Seq,TTTGCAAA,ACACATAT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725425,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296969,0,6050STDY14355633,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +5,69725426,6050STDY14355634,,CTTAGAGT,GAACCCTG,,Duplex-Seq,CTTAGAGT,GAACCCTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725426,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296970,0,6050STDY14355634,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +5,69725427,6050STDY14355635,,GGTGGGAA,TAAACCCA,,Duplex-Seq,GGTGGGAA,TAAACCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725427,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296971,0,6050STDY14355635,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +5,69725428,6050STDY14355636,,CCTCCTAA,ATGCACTG,,Duplex-Seq,CCTCCTAA,ATGCACTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725428,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296972,0,6050STDY14355636,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +5,69725429,6050STDY14355637,,TTTCCAGT,ATGCCAAA,,Duplex-Seq,TTTCCAGT,ATGCCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725429,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296973,0,6050STDY14355637,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),11, +5,69725430,6050STDY14355638,,GATATGTG,CCTACTAA,,Duplex-Seq,GATATGTG,CCTACTAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725430,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296974,0,6050STDY14355638,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),12, +5,69725431,6050STDY14355639,,CATGAATC,ATAAACTT,,Duplex-Seq,CATGAATC,ATAAACTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725431,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296975,0,6050STDY14355639,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),13, +5,69725432,6050STDY14355640,,AGTAGTAG,AGGCCGTT,,Duplex-Seq,AGTAGTAG,AGGCCGTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725432,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296976,0,6050STDY14355640,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),14, +5,69725433,6050STDY14355641,,GAGGGCCG,ACCCTCCA,,Duplex-Seq,GAGGGCCG,ACCCTCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725433,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296977,0,6050STDY14355641,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),15, +5,69725434,6050STDY14355642,,TTGTCCAA,CGGATCCC,,Duplex-Seq,TTGTCCAA,CGGATCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725434,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296978,0,6050STDY14355642,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),16, +5,69725435,6050STDY14355643,,CGCAACTG,TGCCATCC,,Duplex-Seq,CGCAACTG,TGCCATCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725435,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296979,0,6050STDY14355643,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),17, +5,69725436,6050STDY14355644,,CATATTCT,CGGACAAG,,Duplex-Seq,CATATTCT,CGGACAAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725436,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296980,0,6050STDY14355644,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_Macthed,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),18, +5,69725437,6050STDY14355645,,GCGGAGAC,CATTGCAC,,Duplex-Seq,GCGGAGAC,CATTGCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725437,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296981,0,6050STDY14355645,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),19, +5,69725438,6050STDY14355646,,TTGGGTGA,ATAAAGCG,,Duplex-Seq,TTGGGTGA,ATAAAGCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725438,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296982,0,6050STDY14355646,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),20, +5,69725439,6050STDY14355647,,GTTCAAAG,TGCATAAA,,Duplex-Seq,GTTCAAAG,TGCATAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725439,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296983,0,6050STDY14355647,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),21, +5,69725440,6050STDY14355648,,TTAACTTA,GTCATCCT,,Duplex-Seq,TTAACTTA,GTCATCCT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004577,0,69725440,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296984,0,6050STDY14355648,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),22, +5,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004577,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +6,69725419,6050STDY14355627,,CGGAGACA,ATGCGACT,,Duplex-Seq,CGGAGACA,ATGCGACT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725419,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296963,0,6050STDY14355627,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),1, +6,69725420,6050STDY14355628,,GTTAACGT,TCACAAAC,,Duplex-Seq,GTTAACGT,TCACAAAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725420,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296964,0,6050STDY14355628,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),2, +6,69725421,6050STDY14355629,,CATTTATT,AGGAGAAA,,Duplex-Seq,CATTTATT,AGGAGAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725421,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296965,0,6050STDY14355629,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),3, +6,69725422,6050STDY14355630,,TTAGCGCA,TCGGCAAA,,Duplex-Seq,TTAGCGCA,TCGGCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725422,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296966,0,6050STDY14355630,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),4, +6,69725423,6050STDY14355631,,TATTCGTA,CTGAAAGA,,Duplex-Seq,TATTCGTA,CTGAAAGA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725423,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296967,0,6050STDY14355631,,Homo_sapiens (1000Genomes_hs37d5),ShearingNS_Matched,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),5, +6,69725424,6050STDY14355632,,CTAACTAG,GAAAGGTA,,Duplex-Seq,CTAACTAG,GAAAGGTA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725424,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296968,0,6050STDY14355632,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),6, +6,69725425,6050STDY14355633,,TTTGCAAA,ACACATAT,,Duplex-Seq,TTTGCAAA,ACACATAT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725425,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296969,0,6050STDY14355633,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),7, +6,69725426,6050STDY14355634,,CTTAGAGT,GAACCCTG,,Duplex-Seq,CTTAGAGT,GAACCCTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725426,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296970,0,6050STDY14355634,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),8, +6,69725427,6050STDY14355635,,GGTGGGAA,TAAACCCA,,Duplex-Seq,GGTGGGAA,TAAACCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725427,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296971,0,6050STDY14355635,,Homo_sapiens (1000Genomes_hs37d5),ShearingUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),9, +6,69725428,6050STDY14355636,,CCTCCTAA,ATGCACTG,,Duplex-Seq,CCTCCTAA,ATGCACTG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725428,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296972,0,6050STDY14355636,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),10, +6,69725429,6050STDY14355637,,TTTCCAGT,ATGCCAAA,,Duplex-Seq,TTTCCAGT,ATGCCAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725429,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296973,0,6050STDY14355637,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),11, +6,69725430,6050STDY14355638,,GATATGTG,CCTACTAA,,Duplex-Seq,GATATGTG,CCTACTAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725430,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296974,0,6050STDY14355638,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),12, +6,69725431,6050STDY14355639,,CATGAATC,ATAAACTT,,Duplex-Seq,CATGAATC,ATAAACTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725431,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296975,0,6050STDY14355639,,Homo_sapiens (1000Genomes_hs37d5),USNS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),13, +6,69725432,6050STDY14355640,,AGTAGTAG,AGGCCGTT,,Duplex-Seq,AGTAGTAG,AGGCCGTT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725432,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296976,0,6050STDY14355640,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),14, +6,69725433,6050STDY14355641,,GAGGGCCG,ACCCTCCA,,Duplex-Seq,GAGGGCCG,ACCCTCCA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725433,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296977,0,6050STDY14355641,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),15, +6,69725434,6050STDY14355642,,TTGTCCAA,CGGATCCC,,Duplex-Seq,TTGTCCAA,CGGATCCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725434,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296978,0,6050STDY14355642,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),16, +6,69725435,6050STDY14355643,,CGCAACTG,TGCCATCC,,Duplex-Seq,CGCAACTG,TGCCATCC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725435,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296979,0,6050STDY14355643,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),17, +6,69725436,6050STDY14355644,,CATATTCT,CGGACAAG,,Duplex-Seq,CATATTCT,CGGACAAG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725436,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296980,0,6050STDY14355644,,Homo_sapiens (1000Genomes_hs37d5),R1.1NS_Macthed,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),18, +6,69725437,6050STDY14355645,,GCGGAGAC,CATTGCAC,,Duplex-Seq,GCGGAGAC,CATTGCAC,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725437,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296981,0,6050STDY14355645,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),19, +6,69725438,6050STDY14355646,,TTGGGTGA,ATAAAGCG,,Duplex-Seq,TTGGGTGA,ATAAAGCG,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725438,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296982,0,6050STDY14355646,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF3PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),20, +6,69725439,6050STDY14355647,,GTTCAAAG,TGCATAAA,,Duplex-Seq,GTTCAAAG,TGCATAAA,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725439,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296983,0,6050STDY14355647,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),21, +6,69725440,6050STDY14355648,,TTAACTTA,GTCATCCT,,Duplex-Seq,TTAACTTA,GTCATCCT,user1@my.com user2@my.com user3@my.com user4@my.com ,user1@my.com user1@my.com user4@my.com user4@my.com ,user2@my.com user2@my.com user3@my.com user3@my.com,user4@my.com user4@my.com,,0,0,70004578,0,69725440,,9606,S4360,,,standard,,,from:200 to:1500,,,Homo sapiens,0,,,PD37586k,9296984,0,6050STDY14355648,,Homo_sapiens (1000Genomes_hs37d5),USUII_FF17PE,888,EGAS00001004066,1,0,0,Bottleneck sequencing of human tissue.,6050,Bottleneck Sequencing of Human Tissue - (WGS),Homo_sapiens (1000Genomes_hs37d5),0,Bottleneck Sequencing Of Human Tissue (Wgs),22, +6,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004578,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +7,69510840,EGAN00001321692,,CCGCGGTT,AGCGCTAG,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGCGGTT,AGCGCTAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510840,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321692,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5407888,1497836,,DDD_MAIN5407888,,,DDD_1_FR00569506,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,1, +7,69510852,EGAN00002042187,,TTATAACC,GATATCGA,Twist_Human_Core_Exome_BI,Twist Pulldown,TTATAACC,GATATCGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510852,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042187,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5710659,1823623,,DDD_MAIN5710659,,,DDD_1_FR00569278,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,2, +7,69510864,EGAN00001298465,,GGACTTGG,CGCAGACG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGACTTGG,CGCAGACG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510864,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298465,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5867091,2001421,,DDD_MAIN5867091,,,DDD_1_D500PK129595,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,3, +7,69510876,EGAN00001300772,,AAGTCCAA,TATGAGTA,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGTCCAA,TATGAGTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510876,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300772,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908944,2050909,,DDD_MAIN5908944,,,DDD_1_D500PK129441,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,4, +7,69510888,EGAN00001300773,,ATCCACTG,AGGTGCGT,Twist_Human_Core_Exome_BI,Twist Pulldown,ATCCACTG,AGGTGCGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510888,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300773,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908952,2050917,,DDD_MAIN5908952,,,DDD_1_D500PK129440,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,5, +7,69510900,EGAN00001301174,,GCTTGTCA,GAACATAC,Twist_Human_Core_Exome_BI,Twist Pulldown,GCTTGTCA,GAACATAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510900,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001301174,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5966748,2115694,,DDD_MAIN5966748,,,DDD_1_D500PK128034,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,6, +7,69510924,EGAN00001304327,,TGGATCGA,GTGCGATA,Twist_Human_Core_Exome_BI,Twist Pulldown,TGGATCGA,GTGCGATA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510924,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304327,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6029045,2203893,,DDD_MAIN6029045,,,DDD_1_D0RG141038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,7, +7,69510889,EGAN00001293788,,CCAAGTCT,AAGGATGA,Twist_Human_Core_Exome_BI,Twist Pulldown,CCAAGTCT,AAGGATGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510889,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293788,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5678531,1788223,,DDD_MAIN5678531,,,DDD_1_D575PK144581,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,8, +7,69510901,EGAN00001304217,,TTGGACTC,GGAAGCAG,Twist_Human_Core_Exome_BI,Twist Pulldown,TTGGACTC,GGAAGCAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510901,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304217,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6028474,2203237,,DDD_MAIN6028474,,,DDD_1_FR03967352,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,9, +7,69510913,EGAN00001293786,,GGCTTAAG,TCGTGACC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCTTAAG,TCGTGACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510913,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293786,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670657,1779062,,DDD_MAIN5670657,,,DDD_1_D500PK132121,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,10, +7,69510925,EGAN00001293787,,AATCCGGA,CTACAGTT,Twist_Human_Core_Exome_BI,Twist Pulldown,AATCCGGA,CTACAGTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510925,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293787,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670663,1779068,,DDD_MAIN5670663,,,DDD_1_D500PK132132,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,11, +7,69510842,EGAN00001321167,,TAATACAG,ATATTCAC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAATACAG,ATATTCAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510842,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321167,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5426807,1517975,,DDD_MAIN5426807,,,DDD_1_FR00569436,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,12, +7,69510854,EGAN00002042190,,CGGCGTGA,GCGCCTGT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGCGTGA,GCGCCTGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510854,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042190,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5714029,1828207,,DDD_MAIN5714029,,,DDD_1_FR00559472,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,13, +7,69510866,EGAN00001298517,,ATGTAAGT,ACTCTATG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGTAAGT,ACTCTATG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510866,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298517,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908825,2050790,,DDD_MAIN5908825,,,DDD_1_D575NB050268,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,14, +7,69510878,EGAN00003580492,,GCACGGAC,GTCTCGCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCACGGAC,GTCTCGCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510878,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580492,,Homo Sapiens,0,,,6278STDY12901037,8350874,0,6278STDY12901037,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0086,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,15, +7,69510890,EGAN00003580498,,GGTACCTT,AAGACGTC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGTACCTT,AAGACGTC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510890,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580498,,Homo Sapiens,0,,,6278STDY12901046,8350881,0,6278STDY12901046,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0025,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,16, +7,69510902,EGAN00003580503,,AACGTTCC,GGAGTACT,Twist_Human_Core_Exome_BI,Twist Pulldown,AACGTTCC,GGAGTACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510902,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580503,,Homo Sapiens,0,,,6278STDY12901051,8350885,0,6278STDY12901051,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0529,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,17, +7,69510914,EGAN00003580513,,GCAGAATT,ACCGGCCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCAGAATT,ACCGGCCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510914,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580513,,Homo Sapiens,0,,,6278STDY12901061,8350893,0,6278STDY12901061,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5040,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,18, +7,69510926,EGAN00003580516,,ATGAGGCC,GTTAATTG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGAGGCC,GTTAATTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510926,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580516,,Homo Sapiens,0,,,6278STDY12901069,8350899,0,6278STDY12901069,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5014,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,19, +7,69510843,EGAN00003580522,,ACTAAGAT,AACCGCGG,Twist_Human_Core_Exome_BI,Twist Pulldown,ACTAAGAT,AACCGCGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510843,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580522,,Homo Sapiens,0,,,6278STDY12901078,8350904,0,6278STDY12901078,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5031,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,20, +7,69510855,EGAN00003580559,,GTCGGAGC,GGTTATAA,Twist_Human_Core_Exome_BI,Twist Pulldown,GTCGGAGC,GGTTATAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510855,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580559,,Homo Sapiens,0,,,6278STDY12901100,8350921,0,6278STDY12901100,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_1550,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,21, +7,69510867,EGAN00003580560,,CTTGGTAT,CCAAGTCC,Twist_Human_Core_Exome_BI,Twist Pulldown,CTTGGTAT,CCAAGTCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510867,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580560,,Homo Sapiens,0,,,6278STDY12901101,8350922,0,6278STDY12901101,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,22, +7,69510879,EGAN00003581911,,TCCAACGC,TTGGACTT,Twist_Human_Core_Exome_BI,Twist Pulldown,TCCAACGC,TTGGACTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510879,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581911,,Homo Sapiens,0,,,6278STDY12902768,8352273,0,6278STDY12902768,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0346,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,23, +7,69510891,EGAN00003581913,,CCGTGAAG,CAGTGGAT,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGTGAAG,CAGTGGAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510891,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581913,,Homo Sapiens,0,,,6278STDY12902770,8352275,0,6278STDY12902770,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0324,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,24, +7,69510903,EGAN00003581920,,TTACAGGA,TGACAAGC,Twist_Human_Core_Exome_BI,Twist Pulldown,TTACAGGA,TGACAAGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510903,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581920,,Homo Sapiens,0,,,6278STDY12902777,8352282,0,6278STDY12902777,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0335,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,25, +7,69510915,EGAN00003581923,,GGCATTCT,CTAGCTTG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCATTCT,CTAGCTTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510915,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581923,,Homo Sapiens,0,,,6278STDY12902780,8352285,0,6278STDY12902780,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0301,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,26, +7,69510844,EGAN00003581941,,TACCGAGG,CCTGAACT,Twist_Human_Core_Exome_BI,Twist Pulldown,TACCGAGG,CCTGAACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510844,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581941,,Homo Sapiens,0,,,6278STDY12902798,8352303,0,6278STDY12902798,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0398,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,27, +7,69510868,EGAN00003581945,,AGCCTCAT,AGTAGAGA,Twist_Human_Core_Exome_BI,Twist Pulldown,AGCCTCAT,AGTAGAGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510868,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581945,,Homo Sapiens,0,,,6278STDY12902802,8352307,0,6278STDY12902802,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0383,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,28, +7,69510880,EGAN00003581946,,GATTCTGC,GACGAGAG,Twist_Human_Core_Exome_BI,Twist Pulldown,GATTCTGC,GACGAGAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510880,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581946,,Homo Sapiens,0,,,6278STDY12902803,8352308,0,6278STDY12902803,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0372,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,29, +7,69510892,EGAN00003581951,,TCGTAGTG,AGACTTGG,Twist_Human_Core_Exome_BI,Twist Pulldown,TCGTAGTG,AGACTTGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510892,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581951,,Homo Sapiens,0,,,6278STDY12902808,8352313,0,6278STDY12902808,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0395,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,30, +7,69510904,EGAN00003581955,,CTACGACA,GAGTCCAA,Twist_Human_Core_Exome_BI,Twist Pulldown,CTACGACA,GAGTCCAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510904,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581955,,Homo Sapiens,0,,,6278STDY12902811,8352316,0,6278STDY12902811,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0362,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,31, +7,69510916,EGAN00003581958,,TAAGTGGT,CTTAAGCC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAAGTGGT,CTTAAGCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510916,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581958,,Homo Sapiens,0,,,6278STDY12902815,8352320,0,6278STDY12902815,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0396,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,32, +7,69510928,EGAN00003581970,,CGGACAAC,TCCGGATT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGACAAC,TCCGGATT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510928,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581970,,Homo Sapiens,0,,,6278STDY12902827,8352332,0,6278STDY12902827,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0332,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,33, +7,69510845,EGAN00003581974,,ATATGGAT,CTGTATTA,Twist_Human_Core_Exome_BI,Twist Pulldown,ATATGGAT,CTGTATTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510845,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581974,,Homo Sapiens,0,,,6278STDY12902831,8352336,0,6278STDY12902831,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0376,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,34, +7,69510857,EGAN00003581980,,GCGCAAGC,TCACGCCG,Twist_Human_Core_Exome_BI,Twist Pulldown,GCGCAAGC,TCACGCCG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510857,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581980,,Homo Sapiens,0,,,6278STDY12902837,8352342,0,6278STDY12902837,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0379,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,35, +7,69510869,EGAN00003581983,,AAGATACT,ACTTACAT,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGATACT,ACTTACAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510869,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581983,,Homo Sapiens,0,,,6278STDY12902840,8352345,0,6278STDY12902840,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0355,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,36, +7,69510881,EGAN00003581988,,GGAGCGTC,GTCCGTGC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGAGCGTC,GTCCGTGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510881,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581988,,Homo Sapiens,0,,,6278STDY12902845,8352350,0,6278STDY12902845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0361,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,37, +7,69510893,EGAN00003582081,,ATGGCATG,AAGGTACC,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGGCATG,AAGGTACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004572,0,69510893,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003582081,,Homo Sapiens,0,,,6278STDY12902847,8352352,0,6278STDY12902847,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0368,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,38, +7,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004572,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, +8,69510840,EGAN00001321692,,CCGCGGTT,AGCGCTAG,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGCGGTT,AGCGCTAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510840,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321692,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5407888,1497836,,DDD_MAIN5407888,,,DDD_1_FR00569506,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,1, +8,69510852,EGAN00002042187,,TTATAACC,GATATCGA,Twist_Human_Core_Exome_BI,Twist Pulldown,TTATAACC,GATATCGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510852,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042187,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5710659,1823623,,DDD_MAIN5710659,,,DDD_1_FR00569278,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,2, +8,69510864,EGAN00001298465,,GGACTTGG,CGCAGACG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGACTTGG,CGCAGACG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510864,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298465,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5867091,2001421,,DDD_MAIN5867091,,,DDD_1_D500PK129595,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,3, +8,69510876,EGAN00001300772,,AAGTCCAA,TATGAGTA,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGTCCAA,TATGAGTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510876,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300772,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908944,2050909,,DDD_MAIN5908944,,,DDD_1_D500PK129441,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,4, +8,69510888,EGAN00001300773,,ATCCACTG,AGGTGCGT,Twist_Human_Core_Exome_BI,Twist Pulldown,ATCCACTG,AGGTGCGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510888,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001300773,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908952,2050917,,DDD_MAIN5908952,,,DDD_1_D500PK129440,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,5, +8,69510900,EGAN00001301174,,GCTTGTCA,GAACATAC,Twist_Human_Core_Exome_BI,Twist Pulldown,GCTTGTCA,GAACATAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510900,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001301174,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5966748,2115694,,DDD_MAIN5966748,,,DDD_1_D500PK128034,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,6, +8,69510924,EGAN00001304327,,TGGATCGA,GTGCGATA,Twist_Human_Core_Exome_BI,Twist Pulldown,TGGATCGA,GTGCGATA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510924,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304327,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6029045,2203893,,DDD_MAIN6029045,,,DDD_1_D0RG141038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,7, +8,69510889,EGAN00001293788,,CCAAGTCT,AAGGATGA,Twist_Human_Core_Exome_BI,Twist Pulldown,CCAAGTCT,AAGGATGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510889,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293788,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5678531,1788223,,DDD_MAIN5678531,,,DDD_1_D575PK144581,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,8, +8,69510901,EGAN00001304217,,TTGGACTC,GGAAGCAG,Twist_Human_Core_Exome_BI,Twist Pulldown,TTGGACTC,GGAAGCAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510901,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001304217,DDD_cohort,Homo sapiens,0,,,DDD_MAIN6028474,2203237,,DDD_MAIN6028474,,,DDD_1_FR03967352,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,9, +8,69510913,EGAN00001293786,,GGCTTAAG,TCGTGACC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCTTAAG,TCGTGACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510913,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293786,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670657,1779062,,DDD_MAIN5670657,,,DDD_1_D500PK132121,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,10, +8,69510925,EGAN00001293787,,AATCCGGA,CTACAGTT,Twist_Human_Core_Exome_BI,Twist Pulldown,AATCCGGA,CTACAGTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510925,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001293787,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5670663,1779068,,DDD_MAIN5670663,,,DDD_1_D500PK132132,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,11, +8,69510842,EGAN00001321167,,TAATACAG,ATATTCAC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAATACAG,ATATTCAC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510842,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001321167,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5426807,1517975,,DDD_MAIN5426807,,,DDD_1_FR00569436,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,12, +8,69510854,EGAN00002042190,,CGGCGTGA,GCGCCTGT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGCGTGA,GCGCCTGT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510854,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00002042190,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5714029,1828207,,DDD_MAIN5714029,,,DDD_1_FR00559472,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,13, +8,69510866,EGAN00001298517,,ATGTAAGT,ACTCTATG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGTAAGT,ACTCTATG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510866,Homo sapiens,9606,S4215,,,standard,,,from:100 to:400,EGAN00001298517,DDD_cohort,Homo sapiens,0,,,DDD_MAIN5908825,2050790,,DDD_MAIN5908825,,,DDD_1_D575NB050268,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,14, +8,69510878,EGAN00003580492,,GCACGGAC,GTCTCGCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCACGGAC,GTCTCGCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510878,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580492,,Homo Sapiens,0,,,6278STDY12901037,8350874,0,6278STDY12901037,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0086,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,15, +8,69510890,EGAN00003580498,,GGTACCTT,AAGACGTC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGTACCTT,AAGACGTC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510890,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580498,,Homo Sapiens,0,,,6278STDY12901046,8350881,0,6278STDY12901046,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0025,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,16, +8,69510902,EGAN00003580503,,AACGTTCC,GGAGTACT,Twist_Human_Core_Exome_BI,Twist Pulldown,AACGTTCC,GGAGTACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510902,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580503,,Homo Sapiens,0,,,6278STDY12901051,8350885,0,6278STDY12901051,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_0529,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,17, +8,69510914,EGAN00003580513,,GCAGAATT,ACCGGCCA,Twist_Human_Core_Exome_BI,Twist Pulldown,GCAGAATT,ACCGGCCA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510914,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580513,,Homo Sapiens,0,,,6278STDY12901061,8350893,0,6278STDY12901061,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5040,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,18, +8,69510926,EGAN00003580516,,ATGAGGCC,GTTAATTG,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGAGGCC,GTTAATTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510926,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580516,,Homo Sapiens,0,,,6278STDY12901069,8350899,0,6278STDY12901069,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5014,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,19, +8,69510843,EGAN00003580522,,ACTAAGAT,AACCGCGG,Twist_Human_Core_Exome_BI,Twist Pulldown,ACTAAGAT,AACCGCGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510843,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580522,,Homo Sapiens,0,,,6278STDY12901078,8350904,0,6278STDY12901078,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5031,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,20, +8,69510855,EGAN00003580559,,GTCGGAGC,GGTTATAA,Twist_Human_Core_Exome_BI,Twist Pulldown,GTCGGAGC,GGTTATAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510855,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580559,,Homo Sapiens,0,,,6278STDY12901100,8350921,0,6278STDY12901100,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM06_1550,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,21, +8,69510867,EGAN00003580560,,CTTGGTAT,CCAAGTCC,Twist_Human_Core_Exome_BI,Twist Pulldown,CTTGGTAT,CCAAGTCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510867,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003580560,,Homo Sapiens,0,,,6278STDY12901101,8350922,0,6278STDY12901101,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),GM05_5038,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,22, +8,69510879,EGAN00003581911,,TCCAACGC,TTGGACTT,Twist_Human_Core_Exome_BI,Twist Pulldown,TCCAACGC,TTGGACTT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510879,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581911,,Homo Sapiens,0,,,6278STDY12902768,8352273,0,6278STDY12902768,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0346,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,23, +8,69510891,EGAN00003581913,,CCGTGAAG,CAGTGGAT,Twist_Human_Core_Exome_BI,Twist Pulldown,CCGTGAAG,CAGTGGAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510891,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581913,,Homo Sapiens,0,,,6278STDY12902770,8352275,0,6278STDY12902770,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0324,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,24, +8,69510903,EGAN00003581920,,TTACAGGA,TGACAAGC,Twist_Human_Core_Exome_BI,Twist Pulldown,TTACAGGA,TGACAAGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510903,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581920,,Homo Sapiens,0,,,6278STDY12902777,8352282,0,6278STDY12902777,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0335,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,25, +8,69510915,EGAN00003581923,,GGCATTCT,CTAGCTTG,Twist_Human_Core_Exome_BI,Twist Pulldown,GGCATTCT,CTAGCTTG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510915,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581923,,Homo Sapiens,0,,,6278STDY12902780,8352285,0,6278STDY12902780,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0301,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,26, +8,69510844,EGAN00003581941,,TACCGAGG,CCTGAACT,Twist_Human_Core_Exome_BI,Twist Pulldown,TACCGAGG,CCTGAACT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510844,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581941,,Homo Sapiens,0,,,6278STDY12902798,8352303,0,6278STDY12902798,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0398,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,27, +8,69510868,EGAN00003581945,,AGCCTCAT,AGTAGAGA,Twist_Human_Core_Exome_BI,Twist Pulldown,AGCCTCAT,AGTAGAGA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510868,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581945,,Homo Sapiens,0,,,6278STDY12902802,8352307,0,6278STDY12902802,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0383,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,28, +8,69510880,EGAN00003581946,,GATTCTGC,GACGAGAG,Twist_Human_Core_Exome_BI,Twist Pulldown,GATTCTGC,GACGAGAG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510880,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581946,,Homo Sapiens,0,,,6278STDY12902803,8352308,0,6278STDY12902803,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0372,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,29, +8,69510892,EGAN00003581951,,TCGTAGTG,AGACTTGG,Twist_Human_Core_Exome_BI,Twist Pulldown,TCGTAGTG,AGACTTGG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510892,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581951,,Homo Sapiens,0,,,6278STDY12902808,8352313,0,6278STDY12902808,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0395,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,30, +8,69510904,EGAN00003581955,,CTACGACA,GAGTCCAA,Twist_Human_Core_Exome_BI,Twist Pulldown,CTACGACA,GAGTCCAA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510904,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581955,,Homo Sapiens,0,,,6278STDY12902811,8352316,0,6278STDY12902811,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0362,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,31, +8,69510916,EGAN00003581958,,TAAGTGGT,CTTAAGCC,Twist_Human_Core_Exome_BI,Twist Pulldown,TAAGTGGT,CTTAAGCC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510916,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581958,,Homo Sapiens,0,,,6278STDY12902815,8352320,0,6278STDY12902815,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0396,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,32, +8,69510928,EGAN00003581970,,CGGACAAC,TCCGGATT,Twist_Human_Core_Exome_BI,Twist Pulldown,CGGACAAC,TCCGGATT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510928,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581970,,Homo Sapiens,0,,,6278STDY12902827,8352332,0,6278STDY12902827,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0332,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,33, +8,69510845,EGAN00003581974,,ATATGGAT,CTGTATTA,Twist_Human_Core_Exome_BI,Twist Pulldown,ATATGGAT,CTGTATTA,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510845,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581974,,Homo Sapiens,0,,,6278STDY12902831,8352336,0,6278STDY12902831,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0376,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,34, +8,69510857,EGAN00003581980,,GCGCAAGC,TCACGCCG,Twist_Human_Core_Exome_BI,Twist Pulldown,GCGCAAGC,TCACGCCG,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510857,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581980,,Homo Sapiens,0,,,6278STDY12902837,8352342,0,6278STDY12902837,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0379,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,35, +8,69510869,EGAN00003581983,,AAGATACT,ACTTACAT,Twist_Human_Core_Exome_BI,Twist Pulldown,AAGATACT,ACTTACAT,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510869,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581983,,Homo Sapiens,0,,,6278STDY12902840,8352345,0,6278STDY12902840,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0355,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,36, +8,69510881,EGAN00003581988,,GGAGCGTC,GTCCGTGC,Twist_Human_Core_Exome_BI,Twist Pulldown,GGAGCGTC,GTCCGTGC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510881,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003581988,,Homo Sapiens,0,,,6278STDY12902845,8352350,0,6278STDY12902845,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0361,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,37, +8,69510893,EGAN00003582081,,ATGGCATG,AAGGTACC,Twist_Human_Core_Exome_BI,Twist Pulldown,ATGGCATG,AAGGTACC,user6@my.com,user6@my.com,user7@my.com,,0,0,70004571,0,69510893,,9606,S4215,,,standard,,,from:100 to:400,EGAN00003582081,,Homo Sapiens,0,,,6278STDY12902847,8352352,0,6278STDY12902847,,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),OG08_0368,888,EGAS00001005007,1,0,0,Whole exome sequencing of patients with Inflammatory Bowel Disease,6278,HG_WC10130_IBD Bioresource Whole Exome Sequencing of 20%2C000 samples,Homo_sapiens (GRCh38_full_analysis_set_plus_decoy_hla),1,IBD Whole Exome Sequencing ,38, +8,51702674,phiX_for_spiked_buffers,,TGTGCAGC,ACTGATGT,,,TGTGCAGC,ACTGATGT,,,,,,1,0,70004571,0,51702674,,10847,,,,standard,,,,,,,0,,,,1255141,,phiX_for_spiked_buffers,,PhiX (Sanger-SNPs),,888,,1,0,0,None,198,Illumina Controls, ,0,,888, From 6d500bfae44ba7813f372654c046f6fd66ebada5 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Wed, 22 Nov 2023 16:17:43 +0000 Subject: [PATCH 30/35] Ensure insert size is returned for compositions. --- lib/st/api/lims.pm | 2 +- t/40-st-lims.t | 20 +++++++++++++++++--- 2 files changed, 18 insertions(+), 4 deletions(-) diff --git a/lib/st/api/lims.pm b/lib/st/api/lims.pm index 89a76ebd..2e9aac45 100644 --- a/lib/st/api/lims.pm +++ b/lib/st/api/lims.pm @@ -498,7 +498,7 @@ sub _build_required_insert_size { my $self = shift; my $is_hash = {}; - if (defined $self->position) { + if (defined $self->position or defined $self->rpt_list) { my @alims = $self->descendants; @alims = @alims ? @alims : ($self); foreach my $lims (@alims) { diff --git a/t/40-st-lims.t b/t/40-st-lims.t index e9bd09d9..485fbdba 100644 --- a/t/40-st-lims.t +++ b/t/40-st-lims.t @@ -630,7 +630,7 @@ subtest 'Dual index' => sub { }; subtest 'Insert size' => sub { - plan tests => 14; + plan tests => 20; local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = 't/data/samplesheet/4pool4libs_extended.csv'; @@ -657,11 +657,25 @@ subtest 'Insert size' => sub { is ($insert_size->{$id}->{q[to]}, 1000, 'required TO insert size'); ok (!exists $insert_size->{q[6946_7_ACAACGCAAT]}, 'no required insert size'); - $lims = st::api::lims->new(id_run => 9999, position => 7, tag_index => 77); + for my $l (( + st::api::lims->new(id_run => 9999, position => 7, tag_index => 77), + st::api::lims->new(rpt_list => '9999:7:77') + )) { + $insert_size = $l->required_insert_size; + is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); + is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size'); + is ($insert_size->{$id}->{q[to]}, 1000,'required TO insert size'); + } + + local $ENV{NPG_CACHED_SAMPLESHEET_FILE} = + q[t/data/samplesheet/samplesheet_47995.csv]; + + $lims = st::api::lims->new(rpt_list => '47995:1:3;47995:2:3'); $insert_size = $lims->required_insert_size; is (keys %{$insert_size}, 1, 'one entry in the insert size hash'); + $id = '65934645'; is ($insert_size->{$id}->{q[from]}, 100, 'required FROM insert size'); - is ($insert_size->{$id}->{q[to]}, 1000,'required TO insert size'); + is ($insert_size->{$id}->{q[to]}, 400,'required TO insert size'); }; subtest 'Study and sample properties' => sub { From c0ca4eb1ae816adee93127b2d9f399337456df3d Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 27 Nov 2023 09:54:41 +0000 Subject: [PATCH 31/35] Added records for undocumented changed. --- Changes | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/Changes b/Changes index aa0fbee5..d91b9fb1 100644 --- a/Changes +++ b/Changes @@ -18,10 +18,20 @@ LIST OF CHANGES definitions like this have not been in use for the last six years; - reimplemented the 'reference_genome' method to exclude a fallback to a study reference for tag zero and lane-level objects when samples - have different references. - - Restricted the 'all_lanes_mergeable' flag in the 'long_info' role to - NovaSeq Standard workflow, ie dropped an additional case of HiSeq Rapid Run - since HiSeq instruments are no longer used. + have different references; + - ensured 'required_insert_size' method works correctly for objects that + are initialised with the 'rpt_list' attribute, ie have the 'position' + attribute undefined; + - added 'aggregate_libraries' method, which is similar to the existing + 'aggregate_xlanes' method, but instead of getting an instruction to + merge libraries, discovers the libraries which can be merged and returns + a list of merged entities and, separately, a list of singletons. + - npg_tracking::illumina::run::long_info role: + - restricted the 'all_lanes_mergeable' flag to NovaSeq Standard workflow, + ie dropped an additional case of HiSeq Rapid Run since HiSeq instruments + are no longer in use; + - ensured the detection of NovaSeqX and NovaSeq instrument types is + unambiguous. - Updated DBIx classes from the prod database. Changes are due to the MySQL database server upgrade to v8.+ - Finding the runfolder path - stopped errors being raised when a runfolder @@ -29,6 +39,7 @@ LIST OF CHANGES in 'incoming' (the duplicates in 'incoming' are sometimes created by instruments well after the run was mirrored and the runfolder moved to 'analysis'). The duplicate runfolder in 'incoming' is disregarded'. + - DRAGEN samplesheet generation - limit analysis to human samples only. release 97.0.2 - pin DBD::mysql to 4.050 to keep temp support for old mysql clients From 58e62c7af4d3c6b39deaa8652d28c02133fa9340 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Mon, 27 Nov 2023 17:08:49 +0000 Subject: [PATCH 32/35] Fixed incorrect string comparison --- Changes | 1 + bin/npg_move_runfolder | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/Changes b/Changes index d91b9fb1..55f41d96 100644 --- a/Changes +++ b/Changes @@ -40,6 +40,7 @@ LIST OF CHANGES instruments well after the run was mirrored and the runfolder moved to 'analysis'). The duplicate runfolder in 'incoming' is disregarded'. - DRAGEN samplesheet generation - limit analysis to human samples only. + - Fixed incorrect string comparison in the npg_move_runfolder script. release 97.0.2 - pin DBD::mysql to 4.050 to keep temp support for old mysql clients diff --git a/bin/npg_move_runfolder b/bin/npg_move_runfolder index f43d5d69..b0c99235 100755 --- a/bin/npg_move_runfolder +++ b/bin/npg_move_runfolder @@ -22,7 +22,7 @@ GetOptions ( ); if ($help) { pod2usage(0); } -if (!defined $runfolder_path || $runfolder_path == q[]) { +if (!defined $runfolder_path || $runfolder_path eq q[]) { die "ERROR: --runfolder_path argument is required\n"; } From cfa886a0138a22c7dce37244d2c9ec1f7e48c797 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 28 Nov 2023 16:26:07 +0000 Subject: [PATCH 33/35] Correct propagation of the CI target branch. Name variables consistently. Source dependencies from the branch that is the target. --- .github/workflows/run-tests.yml | 4 ++-- Changes | 2 ++ scripts/install_wsi_dependencies.sh | 4 ++-- 3 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 8f4b9ab3..4f8cca26 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -13,8 +13,8 @@ jobs: env: PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached NPG_LIB: ~/perl5npg # NPG modules installed here, not cached - WTSI_NPG_GITHUB_URL: https://github.com/wtsi-npg - WTSI_NPG_BUILD_BRANCH: ${GITHUB_HEAD_REF} + WSI_NPG_GITHUB_URL: https://github.com/wtsi-npg + WSI_NPG_BUILD_BRANCH: ${GITHUB_TARGET_REF} strategy: diff --git a/Changes b/Changes index 55f41d96..a1788c51 100644 --- a/Changes +++ b/Changes @@ -41,6 +41,8 @@ LIST OF CHANGES 'analysis'). The duplicate runfolder in 'incoming' is disregarded'. - DRAGEN samplesheet generation - limit analysis to human samples only. - Fixed incorrect string comparison in the npg_move_runfolder script. + - Ensure that pull requests to the master branch source dependencies from + master branches (devel branch was hardcoded). release 97.0.2 - pin DBD::mysql to 4.050 to keep temp support for old mysql clients diff --git a/scripts/install_wsi_dependencies.sh b/scripts/install_wsi_dependencies.sh index 9d1e506f..627eccf1 100755 --- a/scripts/install_wsi_dependencies.sh +++ b/scripts/install_wsi_dependencies.sh @@ -22,8 +22,8 @@ for repo in "$@" ; do # Shift off master to appropriate branch (if possible) git ls-remote --heads --exit-code origin "$WSI_NPG_BUILD_BRANCH" && \ - git pull origin "$WSI_NPG_BUILD_BRANCH" && \ - echo "Switched to branch $WSI_NPG_BUILD_BRANCH" + git pull origin "$WSI_NPG_BUILD_BRANCH" && \ + echo "Switched to branch $WSI_NPG_BUILD_BRANCH" repos="$repos /tmp/${repo}.git" done From f4dd641d9255a5c55f9d4e9798dd8793a2a4e631 Mon Sep 17 00:00:00 2001 From: Marina Gourtovaia Date: Tue, 28 Nov 2023 16:42:58 +0000 Subject: [PATCH 34/35] Get the branch name correctly, log the branch name. --- .github/workflows/run-tests.yml | 2 +- scripts/install_wsi_dependencies.sh | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index 4f8cca26..e18cba94 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -14,7 +14,7 @@ jobs: PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached NPG_LIB: ~/perl5npg # NPG modules installed here, not cached WSI_NPG_GITHUB_URL: https://github.com/wtsi-npg - WSI_NPG_BUILD_BRANCH: ${GITHUB_TARGET_REF} + WSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }} strategy: diff --git a/scripts/install_wsi_dependencies.sh b/scripts/install_wsi_dependencies.sh index 627eccf1..975a3c15 100755 --- a/scripts/install_wsi_dependencies.sh +++ b/scripts/install_wsi_dependencies.sh @@ -21,6 +21,7 @@ for repo in "$@" ; do cd "/tmp/${repo}.git" # Shift off master to appropriate branch (if possible) + echo "Want to switch to branch $WSI_NPG_BUILD_BRANCH" git ls-remote --heads --exit-code origin "$WSI_NPG_BUILD_BRANCH" && \ git pull origin "$WSI_NPG_BUILD_BRANCH" && \ echo "Switched to branch $WSI_NPG_BUILD_BRANCH" From 7758a009b936591610bc5a2963a4d83049575871 Mon Sep 17 00:00:00 2001 From: jmtcsngr Date: Thu, 30 Nov 2023 13:56:17 +0000 Subject: [PATCH 35/35] prep release 98.0.0 --- Changes | 1 + 1 file changed, 1 insertion(+) diff --git a/Changes b/Changes index a1788c51..ca1b3b4e 100644 --- a/Changes +++ b/Changes @@ -1,5 +1,6 @@ LIST OF CHANGES +release 98.0.0 - Removed the use of 'xml' lims driver from all tests. - Deleted 'xml' lims driver class and all classes which supported this functionality, together with all related tests and test data.