{
"@context": "/terms/",
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"FileSet",
"Item"
],
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],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8746LSXO](/auxiliary-sets/IGVFDS8746LSXO/) has sequence file(s): [IGVFFI1591CZNR](/sequence-files/IGVFFI1591CZNR/), [IGVFFI7164IWPZ](/sequence-files/IGVFFI7164IWPZ/), [IGVFFI8604OWOL](/sequence-files/IGVFFI8604OWOL/) 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/IGVFDS8746LSXO/"
}
]
},
"award": {
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"component": "functional characterization",
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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": "2023-12-08T23:52:37.715972+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": "IGVFFI1591CZNR",
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],
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"creation_timestamp": "2023-12-09T00:52:20.581483+00:00",
"file_format": "fastq",
"file_size": 299392906,
"href": "/sequence-files/IGVFFI1591CZNR/@@download/IGVFFI1591CZNR.fastq.gz",
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"sequencing_platform": "/platform-terms/EFO_0009173/",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7164IWPZ/",
"accession": "IGVFFI7164IWPZ",
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"creation_timestamp": "2023-12-09T00:52:22.950616+00:00",
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"file_size": 323332408,
"href": "/sequence-files/IGVFFI7164IWPZ/@@download/IGVFFI7164IWPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/ffd7f305-2d8e-40bd-acad-3b5f27754bb4/IGVFFI7164IWPZ.fastq.gz",
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"status": "released",
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},
{
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"creation_timestamp": "2023-12-09T00:52:21.709894+00:00",
"file_format": "fastq",
"file_size": 268668955,
"href": "/sequence-files/IGVFFI8604OWOL/@@download/IGVFFI8604OWOL.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/c236e4df-841d-40b1-8bb4-9adda96ac8bd/IGVFFI8604OWOL.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_rep2B1_d04_DNA_R2_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/IGVFDS8540VFIL/",
"accession": "IGVFDS8540VFIL",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_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": "2024-06-27T00:41:13.079273+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM3811HZXX/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3811HZXX",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_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": [
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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 4 days, male, Mus musculus WD44 transfected with a reporter library",
"targeted_sample_term": {
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"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": "2023-12-09T00:52:20.581483+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "faf19294-71cd-4e7c-95ac-c84244c19f8d"
}