{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
"audit": {
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS2370ZRIR](/auxiliary-sets/IGVFDS2370ZRIR/) has sequence file(s): [IGVFFI6217NSYJ](/sequence-files/IGVFFI6217NSYJ/), [IGVFFI2732UAKI](/sequence-files/IGVFFI2732UAKI/), [IGVFFI9023RNEB](/sequence-files/IGVFFI9023RNEB/) 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/IGVFDS2370ZRIR/"
}
]
},
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"component": "functional characterization",
"contact_pi": {
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"title": "Jay Shendure"
},
"title": "Massively parallel characterization of variants and elements impacting transcriptional regulation in dynamic cellular systems"
},
"control_for": [],
"creation_timestamp": "2023-12-08T23:52:39.795784+00:00",
"donors": [
{
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"accession": "IGVFDO3898MNLZ",
"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
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{
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"content_type": "reads",
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"file_format": "fastq",
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"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_rep2B1_d12_DNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2732UAKI/",
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"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_rep2B1_d12_DNA_R3_001.fastq.gz",
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},
{
"@id": "/sequence-files/IGVFFI9023RNEB/",
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"content_type": "reads",
"creation_timestamp": "2023-12-09T00:52:36.397189+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI9023RNEB/@@download/IGVFFI9023RNEB.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/bf5b82fb-f393-4552-be25-2c15be81275b/IGVFFI9023RNEB.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_rep2B1_d12_DNA_R1_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
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],
"lab": {
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"title": "Jay Shendure, UW"
},
"measurement_sets": [
{
"@id": "/measurement-sets/IGVFDS1416HRTP/",
"accession": "IGVFDS1416HRTP",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_bulk_RNA_day12_reads"
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"preferred_assay_title": "MPRA"
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],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
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"PMID:38724692"
]
}
],
"release_timestamp": "2024-06-27T00:41:17.024493+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM0608PJZS/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0608PJZS",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_bulk_day12"
],
"cell_fate_change_treatments": [
"/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/"
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
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],
"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 12 days, male, Mus musculus WD44 transfected with a reporter library",
"targeted_sample_term": {
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"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": "2023-12-09T00:52:36.397189+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "f83917a6-5218-48d1-ab40-660be6d33f71"
}