{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS6212LCHT/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS6212LCHT",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day12_reads"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS6212LCHT](/auxiliary-sets/IGVFDS6212LCHT/) has sequence file(s): [IGVFFI9129BBIZ](/sequence-files/IGVFFI9129BBIZ/), [IGVFFI4641YKTD](/sequence-files/IGVFFI4641YKTD/), [IGVFFI7420HGJZ](/sequence-files/IGVFFI7420HGJZ/) 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/IGVFDS6212LCHT/"
}
]
},
"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": "2023-12-08T23:52:32.606934+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/IGVFFI9129BBIZ/",
"accession": "IGVFFI9129BBIZ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day12_DNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:33.242029+00:00",
"file_format": "fastq",
"file_size": 119237791,
"href": "/sequence-files/IGVFFI9129BBIZ/@@download/IGVFFI9129BBIZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/d6c6191b-9483-41e1-838e-46986f88b29a/IGVFFI9129BBIZ.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_repB_d12_DNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4641YKTD/",
"accession": "IGVFFI4641YKTD",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day12_DNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:32.063319+00:00",
"file_format": "fastq",
"file_size": 244843871,
"href": "/sequence-files/IGVFFI4641YKTD/@@download/IGVFFI4641YKTD.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/11937772-c48b-4a6e-95a4-2dca53db7d82/IGVFFI4641YKTD.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_repB_d12_DNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7420HGJZ/",
"accession": "IGVFFI7420HGJZ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day12_DNA_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:34.339963+00:00",
"file_format": "fastq",
"file_size": 343154816,
"href": "/sequence-files/IGVFFI7420HGJZ/@@download/IGVFFI7420HGJZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a617a8f7-7711-4a1f-bb8f-929e6a6c72d6/IGVFFI7420HGJZ.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_repB_d12_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/IGVFDS8920YVYN/",
"accession": "IGVFDS8920YVYN",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day12_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": "2024-06-27T00:41:14.605028+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1576AJXB/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1576AJXB",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day12"
],
"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 12 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": "2023-12-09T00:56:32.063319+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "571efce9-599c-496c-af03-8dc4854b0907"
}