{
"@context": "/terms/",
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"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9987GJPC",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day4_reads"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9987GJPC](/auxiliary-sets/IGVFDS9987GJPC/) has sequence file(s): [IGVFFI9313PXEK](/sequence-files/IGVFFI9313PXEK/), [IGVFFI4334ZQRM](/sequence-files/IGVFFI4334ZQRM/), [IGVFFI0349LPOO](/sequence-files/IGVFFI0349LPOO/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS9987GJPC/"
}
]
},
"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": "2023-12-08T23:52:19.965205+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "quantification DNA barcode sequencing",
"files": [
{
"@id": "/sequence-files/IGVFFI9313PXEK/",
"accession": "IGVFFI9313PXEK",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day4_DNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:54:20.783452+00:00",
"file_format": "fastq",
"file_size": 123867138,
"href": "/sequence-files/IGVFFI9313PXEK/@@download/IGVFFI9313PXEK.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/9925a4d0-56f5-453f-b5e6-d185b82174d7/IGVFFI9313PXEK.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/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d04_DNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4334ZQRM/",
"accession": "IGVFFI4334ZQRM",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day4_DNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:54:19.633173+00:00",
"file_format": "fastq",
"file_size": 253568048,
"href": "/sequence-files/IGVFFI4334ZQRM/@@download/IGVFFI4334ZQRM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/f057f641-33e5-48c0-8de1-b826eb5779c2/IGVFFI4334ZQRM.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/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d04_DNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0349LPOO/",
"accession": "IGVFFI0349LPOO",
"aliases": [
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],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:54:21.923099+00:00",
"file_format": "fastq",
"file_size": 350065190,
"href": "/sequence-files/IGVFFI0349LPOO/@@download/IGVFFI0349LPOO.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/b370c1e9-1d5f-428a-8f0b-fcca280dfbcf/IGVFFI0349LPOO.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/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d04_DNA_R3_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2622CKLA/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9853FXPT/",
"accession": "IGVFDS9853FXPT",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day4_reads"
],
"preferred_assay_title": "MPRA",
"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": "2024-06-27T00:41:12.547316+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7613TOIM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7613TOIM",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_day4"
],
"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 4 days, 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": "2023-12-09T00:54:19.633173+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "2a6a4dcb-6945-4d2e-9c52-73e140237d3f"
}