{
"@context": "/terms/",
"@id": "/auxiliary-sets/IGVFDS9488YMYJ/",
"@type": [
"AuxiliarySet",
"FileSet",
"Item"
],
"accession": "IGVFDS9488YMYJ",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day8_reads"
],
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS9488YMYJ](/auxiliary-sets/IGVFDS9488YMYJ/) has sequence file(s): [IGVFFI9693UKRG](/sequence-files/IGVFFI9693UKRG/), [IGVFFI5404ZBPX](/sequence-files/IGVFFI5404ZBPX/), [IGVFFI8186EWAF](/sequence-files/IGVFFI8186EWAF/) 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/IGVFDS9488YMYJ/"
}
],
"WARNING": [
{
"category": "missing read names",
"detail": "MPRA Auxiliary set [IGVFDS9488YMYJ](/auxiliary-sets/IGVFDS9488YMYJ/) links to sequence files: [IGVFFI9693UKRG](/sequence-files/IGVFFI9693UKRG/),[IGVFFI5404ZBPX](/sequence-files/IGVFFI5404ZBPX/),[IGVFFI8186EWAF](/sequence-files/IGVFFI8186EWAF/) that do not specify `read_names`. MPRA measurement set and auxiliary set sequence files are expected to specify a read name.",
"level": 40,
"level_name": "WARNING",
"name": "audit_MPRA_read_names",
"path": "/auxiliary-sets/IGVFDS9488YMYJ/"
}
]
},
"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": "2023-12-08T23:52:31.070921+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/IGVFFI9693UKRG/",
"accession": "IGVFFI9693UKRG",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day8_DNA_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:19.873802+00:00",
"file_format": "fastq",
"file_size": 465225005,
"href": "/sequence-files/IGVFFI9693UKRG/@@download/IGVFFI9693UKRG.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/11b3f5bb-95e1-424c-af74-4d543aead3ba/IGVFFI9693UKRG.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_d08_DNA_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5404ZBPX/",
"accession": "IGVFFI5404ZBPX",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day8_DNA_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:16.534602+00:00",
"file_format": "fastq",
"file_size": 333745826,
"href": "/sequence-files/IGVFFI5404ZBPX/@@download/IGVFFI5404ZBPX.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/a41ac9b6-ab32-4cdc-98a6-a2a4c2b6d6a5/IGVFFI5404ZBPX.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_d08_DNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8186EWAF/",
"accession": "IGVFFI8186EWAF",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repB_day8_DNA_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-12-09T00:56:17.999784+00:00",
"file_format": "fastq",
"file_size": 161460624,
"href": "/sequence-files/IGVFFI8186EWAF/@@download/IGVFFI8186EWAF.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/7cb2e0c6-0f23-4e0e-9432-48453e19b470/IGVFFI8186EWAF.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_d08_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/IGVFDS2172PVLM/",
"accession": "IGVFDS2172PVLM",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day8_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": "2024-06-27T00:41:17.287330+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM5166XVRM/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5166XVRM",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repB_bulk_day8"
],
"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 8 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": "2023-12-09T00:56:16.534602+00:00",
"summary": "quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "c82b88fa-7214-4b25-a4b8-1e28e9350a4b"
}