{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS1156NHWQ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS1156NHWQ",
"aliases": [
"jay-shendure:dev_CRE_mEBs_oBC_repB_10Xlane1_reads"
],
"audit": {},
"award": {
"@id": "/awards/HG011966/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/eb543cda-67b7-493c-84eb-187d0dac13ba/",
"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-08T23:52:15.422215+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "circularized RNA barcode detection",
"files": [
{
"@id": "/sequence-files/IGVFFI5640PFLS/",
"accession": "IGVFFI5640PFLS",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_10Xlane1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:59:07.784513+00:00",
"file_format": "fastq",
"file_size": 187807387,
"href": "/sequence-files/IGVFFI5640PFLS/@@download/IGVFFI5640PFLS.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/b0273a80-80ef-4305-aaf1-42eba636d082/IGVFFI5640PFLS.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9197GQMP/",
"accession": "IGVFFI9197GQMP",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_reseq_10Xlane1_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:59:11.303527+00:00",
"file_format": "fastq",
"file_size": 306249279,
"href": "/sequence-files/IGVFFI9197GQMP/@@download/IGVFFI9197GQMP.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/16078e80-107f-4a02-9143-f57569a7618c/IGVFFI9197GQMP.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_reseq_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7721URJL/",
"accession": "IGVFFI7721URJL",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_10Xlane1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:59:09.040415+00:00",
"file_format": "fastq",
"file_size": 463805765,
"href": "/sequence-files/IGVFFI7721URJL/@@download/IGVFFI7721URJL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/90116fc0-435f-4e4b-937a-dd6d184e700c/IGVFFI7721URJL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3190GFNQ/",
"accession": "IGVFFI3190GFNQ",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_reseq_10Xlane1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:59:13.592732+00:00",
"file_format": "fastq",
"file_size": 723775319,
"href": "/sequence-files/IGVFFI3190GFNQ/@@download/IGVFFI3190GFNQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/d61fcc94-3c79-41c0-b7ef-74bbcc2eaf92/IGVFFI3190GFNQ.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_reseq_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7577NRWF/",
"accession": "IGVFFI7577NRWF",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_10Xlane1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:59:10.273137+00:00",
"file_format": "fastq",
"file_size": 651111535,
"href": "/sequence-files/IGVFFI7577NRWF/@@download/IGVFFI7577NRWF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/60823bcd-c7b1-42da-b904-28abaa99797a/IGVFFI7577NRWF.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5061UUQA/",
"accession": "IGVFFI5061UUQA",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_oBC_CS1_repB_reseq_10Xlane1_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:59:12.491592+00:00",
"file_format": "fastq",
"file_size": 932932385,
"href": "/sequence-files/IGVFFI5061UUQA/@@download/IGVFFI5061UUQA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/87fcc5bd-1337-4f29-af1d-836ded395cca/IGVFFI5061UUQA.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"status": "released",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/sc_rep_devCRE_mEBs/sc_rep_mEB_series_oBC_CS1_repB_lane1_reseq_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9532SVZB/",
"accession": "IGVFFI9532SVZB",
"aliases": [
"jay-shendure:seqspec_of_set_IGVFDS1156NHWQ-reseq"
],
"content_type": "seqspec",
"creation_timestamp": "2024-08-22T22:51:34.627421+00:00",
"file_format": "yaml",
"file_size": 887,
"href": "/configuration-files/IGVFFI9532SVZB/@@download/IGVFFI9532SVZB.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/22/53adb440-1c5e-4c73-89e0-2e887c3e7243/IGVFFI9532SVZB.yaml.gz",
"status": "in progress",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS1156NHWQ_reseq_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4325OITW/",
"accession": "IGVFFI4325OITW",
"aliases": [
"jay-shendure:seqspec_of_set_IGVFDS1156NHWQ"
],
"content_type": "seqspec",
"creation_timestamp": "2024-08-22T22:51:32.150285+00:00",
"file_format": "yaml",
"file_size": 884,
"href": "/configuration-files/IGVFFI4325OITW/@@download/IGVFFI4325OITW.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/22/e336865e-acad-469f-b7ef-194160b3320a/IGVFFI4325OITW.yaml.gz",
"status": "in progress",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS1156NHWQ_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2774OLAH/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS0228POXF/",
"accession": "IGVFDS0228POXF",
"aliases": [
"jay-shendure:dev_CRE_mEBs_GEx_repB_10Xlane1_reads"
],
"preferred_assay_title": "MPRA (scQer)",
"status": "released"
}
],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
"doi:10.1038/s41592-024-02260-3",
"PMID:38724692"
],
"status": "released"
}
],
"release_timestamp": "2024-06-27T00:41:46.317583+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8913GAXO/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8913GAXO",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_10Xlane1"
],
"cell_fate_change_treatments": [
"/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
"/construct-library-sets/IGVFDS7655GRFI/"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0004038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "mouse embryonic stem cell",
"term_name": "mouse embryonic stem cell"
}
],
"status": "released",
"summary": "mouse embryonic stem differentiated cell specimen induced to embryoid body for 21 days (cellular sub pool: 10Xlane1), male, Mus musculus WD44 transfected with a reporter library",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"status": "released",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"schema_version": "12",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:59:07.784513+00:00",
"summary": "circularized RNA barcode detection for MPRA (scQer) integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "878d1268-2155-4997-89cc-13354d03b31e"
}