{
"@context": "/terms/",
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"FileSet",
"Item"
],
"accession": "IGVFDS1135XOEU",
"aliases": [
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],
"audit": {
"WARNING": [
{
"category": "missing read names",
"detail": "MPRA Auxiliary set [IGVFDS1135XOEU](/auxiliary-sets/IGVFDS1135XOEU/) links to sequence files: [IGVFFI7585NXPD](/sequence-files/IGVFFI7585NXPD/),[IGVFFI2544WJNK](/sequence-files/IGVFFI2544WJNK/),[IGVFFI4402ZZGL](/sequence-files/IGVFFI4402ZZGL/) that do not specify `read_names`. MPRA measurement set and auxiliary set sequence files are expected to specify a read name.",
"level": 40,
"level_name": "WARNING",
"name": "audit_MPRA_read_names",
"path": "/auxiliary-sets/IGVFDS1135XOEU/"
}
]
},
"award": {
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"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": "2023-12-08T23:52:12.344870+00:00",
"donors": [
{
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"accession": "IGVFDO3898MNLZ",
"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "quantification DNA barcode sequencing",
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{
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"accession": "IGVFFI7585NXPD",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:21.469289+00:00",
"file_format": "fastq",
"file_size": 275629410,
"href": "/sequence-files/IGVFFI7585NXPD/@@download/IGVFFI7585NXPD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/156ecc80-6701-414c-ba0a-3c9c57834cc5/IGVFFI7585NXPD.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"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_mBC_pdT_rep2B_lane1_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2544WJNK/",
"accession": "IGVFFI2544WJNK",
"aliases": [
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],
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"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:22.670728+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI2544WJNK/@@download/IGVFFI2544WJNK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/b388dda8-9d47-4a27-a9fa-b9ff31064308/IGVFFI2544WJNK.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"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_mBC_pdT_rep2B_lane1_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4402ZZGL/",
"accession": "IGVFFI4402ZZGL",
"aliases": [
"jay-shendure:sc_rep_devCRE_mEBs_mBC_pdT_rep2B_10Xlane1_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:58:23.857571+00:00",
"file_format": "fastq",
"file_size": 828527826,
"href": "/sequence-files/IGVFFI4402ZZGL/@@download/IGVFFI4402ZZGL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/bcb15504-1ea3-44da-928b-6dcce73d7c0c/IGVFFI4402ZZGL.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0008566/",
"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_mBC_pdT_rep2B_lane1_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7564FTZK/",
"accession": "IGVFFI7564FTZK",
"aliases": [
"jay-shendure:seqspec_of_set_IGVFDS1135XOEU"
],
"content_type": "seqspec",
"creation_timestamp": "2024-08-22T22:51:23.720069+00:00",
"file_format": "yaml",
"file_size": 1106,
"href": "/configuration-files/IGVFFI7564FTZK/@@download/IGVFFI7564FTZK.yaml.gz",
"s3_uri": "s3://igvf-files/2024/08/22/eb8eb826-b264-44f7-9c23-2746207c54c5/IGVFFI7564FTZK.yaml.gz",
"status": "in progress",
"submitted_file_name": "/net/shendure/vol1/home/martin91/IGVF/forupload/seqspecs/scQers/scQers_IGVFDS1135XOEU_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/IGVFDS6967XELN/",
"accession": "IGVFDS6967XELN",
"aliases": [
"jay-shendure:dev_CRE_mEBs_GEx_rep2B_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": "2024-06-27T00:41:45.257731+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0317RLIP/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0317RLIP",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_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": "2023-12-09T00:58:21.469289+00:00",
"summary": "quantification DNA barcode sequencing for MPRA (scQer) integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "3f5ad2cf-f583-4e32-a7ef-aed000f034d9"
}