{
"@context": "/terms/",
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"AuxiliarySet",
"FileSet",
"Item"
],
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"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day16_reads"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8780MGRB](/in-vitro-systems/IGVFSM8780MGRB/) has in progress subobject construct library set [IGVFDS7655GRFI](/construct-library-sets/IGVFDS7655GRFI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8780MGRB/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2965JJYR](/auxiliary-sets/IGVFDS2965JJYR/) has sequence file(s): [IGVFFI2907UGPA](/sequence-files/IGVFFI2907UGPA/), [IGVFFI2511SPLG](/sequence-files/IGVFFI2511SPLG/), [IGVFFI2927UCHR](/sequence-files/IGVFFI2927UCHR/), [IGVFFI9412XAYU](/sequence-files/IGVFFI9412XAYU/), [IGVFFI4092ZSXR](/sequence-files/IGVFFI4092ZSXR/), [IGVFFI5253XKCX](/sequence-files/IGVFFI5253XKCX/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS2965JJYR/"
}
]
},
"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": "2023-12-08T23:52:34.364001+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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"sequencing_platform": "/platform-terms/EFO_0010963/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2511SPLG/",
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"creation_timestamp": "2023-12-09T00:56:53.188755+00:00",
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"href": "/sequence-files/IGVFFI2511SPLG/@@download/IGVFFI2511SPLG.fastq.gz",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2927UCHR/",
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"aliases": [
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],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:54.338841+00:00",
"file_format": "fastq",
"file_size": 595720776,
"href": "/sequence-files/IGVFFI2927UCHR/@@download/IGVFFI2927UCHR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/da9584de-1d52-41e4-be75-611688027e04/IGVFFI2927UCHR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d16_DNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9412XAYU/",
"accession": "IGVFFI9412XAYU",
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],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:47.248153+00:00",
"file_format": "fastq",
"file_size": 635341665,
"href": "/sequence-files/IGVFFI9412XAYU/@@download/IGVFFI9412XAYU.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/0184c36a-9394-4cc3-a13d-7ea55553fb3b/IGVFFI9412XAYU.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d16_DNA_extract_lib_rep_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4092ZSXR/",
"accession": "IGVFFI4092ZSXR",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_DNA_addreads_R2"
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"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:48.677460+00:00",
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"href": "/sequence-files/IGVFFI4092ZSXR/@@download/IGVFFI4092ZSXR.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/f7822263-ae1c-4b34-81c1-05245b4f2353/IGVFFI4092ZSXR.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0010963/",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d16_DNA_extract_lib_rep_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5253XKCX/",
"accession": "IGVFFI5253XKCX",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day16_DNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:56:50.937602+00:00",
"file_format": "fastq",
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"s3_uri": "s3://igvf-files/2023/12/09/3c2d9ad6-417f-47a3-826a-c0dedebf5c03/IGVFFI5253XKCX.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repB_d16_DNA_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS2622CKLA/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS9342OPKS/",
"accession": "IGVFDS9342OPKS",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day16_reads"
],
"preferred_assay_title": "MPRA"
}
],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
"doi:10.1038/s41592-024-02260-3",
"PMID:38724692"
]
}
],
"release_timestamp": "2024-06-27T00:41:19.703670+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM8780MGRB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8780MGRB",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day16"
],
"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": [
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"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 16 days, male, Mus musculus WD44 modified with a reporter library",
"targeted_sample_term": {
"@id": "/sample-terms/UBERON_0014374/",
"term_name": "embryoid body"
},
"taxa": "Mus musculus"
}
],
"schema_version": "11",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:56:47.248153+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "e811bd56-cd2d-4c1c-a626-bdd0e66a117e"
}