{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS3976EEWC/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS3976EEWC",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part2_bulk_DNA_day16_reads"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM4092RUKD](/in-vitro-systems/IGVFSM4092RUKD/) 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/IGVFSM4092RUKD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS3976EEWC](/auxiliary-sets/IGVFDS3976EEWC/) has sequence file(s): [IGVFFI4231TRRJ](/sequence-files/IGVFFI4231TRRJ/), [IGVFFI5101QWMQ](/sequence-files/IGVFFI5101QWMQ/), [IGVFFI4680FMML](/sequence-files/IGVFFI4680FMML/) 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/IGVFDS3976EEWC/"
}
]
},
"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": "2023-12-08T23:52:44.863929+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/IGVFFI4231TRRJ/",
"accession": "IGVFFI4231TRRJ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_2_day16_DNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:53:41.772126+00:00",
"file_format": "fastq",
"file_size": 253244742,
"href": "/sequence-files/IGVFFI4231TRRJ/@@download/IGVFFI4231TRRJ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/94c60918-f6a9-422c-b9aa-d4943522174f/IGVFFI4231TRRJ.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_rep2B2_d16_DNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5101QWMQ/",
"accession": "IGVFFI5101QWMQ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_2_day16_DNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:53:43.641040+00:00",
"file_format": "fastq",
"file_size": 228422727,
"href": "/sequence-files/IGVFFI5101QWMQ/@@download/IGVFFI5101QWMQ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/f5eb2762-dfee-47c8-a3bf-d6280d6dafb1/IGVFFI5101QWMQ.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_rep2B2_d16_DNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4680FMML/",
"accession": "IGVFFI4680FMML",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_rep2B_2_day16_DNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:53:44.719431+00:00",
"file_format": "fastq",
"file_size": 274441880,
"href": "/sequence-files/IGVFFI4680FMML/@@download/IGVFFI4680FMML.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/c54f684e-f8c1-4b0c-ae18-073d3cbce85b/IGVFFI4680FMML.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_rep2B2_d16_DNA_R3_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/IGVFDS2106RDJT/",
"accession": "IGVFDS2106RDJT",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part2_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": "2024-06-27T00:41:13.946765+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM4092RUKD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4092RUKD",
"aliases": [
"jay-shendure:dev_CRE_mEBs_rep2B_part2_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": [
"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 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": "2023-12-09T00:53:41.772126+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "907446ed-a3fe-4787-b4c2-6be9807ce9e7"
}