{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6028VFBK/",
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"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6028VFBK",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_bulk_DNA_day0_reads"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6028VFBK](/auxiliary-sets/IGVFDS6028VFBK/) has sequence file(s): [IGVFFI6514GXEM](/sequence-files/IGVFFI6514GXEM/), [IGVFFI0338SLHZ](/sequence-files/IGVFFI0338SLHZ/), [IGVFFI7432PTRM](/sequence-files/IGVFFI7432PTRM/) 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/IGVFDS6028VFBK/"
}
]
},
"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": "2023-12-08T23:52:37.072590+00:00",
"donors": [
{
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"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
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"files": [
{
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"accession": "IGVFFI6514GXEM",
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"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_1_day0_DNA_R3"
],
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"controlled_access": false,
"creation_timestamp": "2023-12-09T00:52:12.619263+00:00",
"file_format": "fastq",
"file_size": 372421025,
"href": "/sequence-files/IGVFFI6514GXEM/@@download/IGVFFI6514GXEM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/6c4e9b5f-e89d-4bf7-8cad-28324dd2bc0c/IGVFFI6514GXEM.fastq.gz",
"sequencing_platform": "/platform-terms/EFO_0009173/",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0338SLHZ/",
"accession": "IGVFFI0338SLHZ",
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"creation_timestamp": "2023-12-09T00:52:11.460942+00:00",
"file_format": "fastq",
"file_size": 307298078,
"href": "/sequence-files/IGVFFI0338SLHZ/@@download/IGVFFI0338SLHZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/74ca4348-bb27-412c-9095-754b8bdf3f35/IGVFFI0338SLHZ.fastq.gz",
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"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_d00_DNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7432PTRM/",
"accession": "IGVFFI7432PTRM",
"aliases": [
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"controlled_access": false,
"creation_timestamp": "2023-12-09T00:52:10.281362+00:00",
"file_format": "fastq",
"file_size": 343286947,
"href": "/sequence-files/IGVFFI7432PTRM/@@download/IGVFFI7432PTRM.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/e8fea387-7227-47f6-b848-44c63af45728/IGVFFI7432PTRM.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_d00_DNA_R1_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/IGVFDS9778WLEE/",
"accession": "IGVFDS9778WLEE",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_bulk_RNA_day0_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": "2024-06-27T00:41:13.512956+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1671CSBE/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1671CSBE",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part1_bulk_day0"
],
"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, 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": "2023-12-09T00:52:10.281362+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "df7e994c-9f19-45f2-990c-5161f75a862d"
}