{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1500XNWW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1500XNWW",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_RNA_day18_reads"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002675/",
"term_name": "massively parallel reporter assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM1019NMFD](/in-vitro-systems/IGVFSM1019NMFD/) 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/IGVFSM1019NMFD/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS4928ZASL](/auxiliary-sets/IGVFDS4928ZASL/) has sequence file(s): [IGVFFI7942DDVG](/sequence-files/IGVFFI7942DDVG/), [IGVFFI2050HBTK](/sequence-files/IGVFFI2050HBTK/), [IGVFFI5707DFNY](/sequence-files/IGVFFI5707DFNY/) 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/IGVFDS4928ZASL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1500XNWW](/measurement-sets/IGVFDS1500XNWW/) has sequence file(s): [IGVFFI2980ZNPZ](/sequence-files/IGVFFI2980ZNPZ/), [IGVFFI7014ELNA](/sequence-files/IGVFFI7014ELNA/), [IGVFFI1218OSBH](/sequence-files/IGVFFI1218OSBH/) 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": "/measurement-sets/IGVFDS1500XNWW/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS4928ZASL/",
"accession": "IGVFDS4928ZASL",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_DNA_day18_reads"
],
"file_set_type": "quantification DNA barcode sequencing"
}
],
"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": "2023-12-08T23:53:58.112971+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3898MNLZ/",
"accession": "IGVFDO3898MNLZ",
"aliases": [
"jay-shendure:WD44_donor"
],
"sex": "male",
"status": "released",
"taxa": "Mus musculus"
}
],
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2980ZNPZ/",
"accession": "IGVFFI2980ZNPZ",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day18_RNA_R1"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:26.951157+00:00",
"file_format": "fastq",
"file_size": 810883073,
"href": "/sequence-files/IGVFFI2980ZNPZ/@@download/IGVFFI2980ZNPZ.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/49586e69-e675-4887-a770-b0063d59807b/IGVFFI2980ZNPZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d18_RNA_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7014ELNA/",
"accession": "IGVFFI7014ELNA",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day18_RNA_R2"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:28.116330+00:00",
"file_format": "fastq",
"file_size": 702986496,
"href": "/sequence-files/IGVFFI7014ELNA/@@download/IGVFFI7014ELNA.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/12e1403f-6d96-4782-b96c-5d055e67e669/IGVFFI7014ELNA.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d18_RNA_R2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1218OSBH/",
"accession": "IGVFFI1218OSBH",
"aliases": [
"jay-shendure:bulkMPRA_devCRE_mEBs_repA_day18_RNA_R3"
],
"content_type": "reads",
"creation_timestamp": "2023-12-09T00:55:29.439509+00:00",
"file_format": "fastq",
"file_size": 821667101,
"href": "/sequence-files/IGVFFI1218OSBH/@@download/IGVFFI1218OSBH.fastq.gz",
"s3_uri": "s3://igvf-files/2023/12/09/e944a875-17db-406a-98b0-31f02820ad21/IGVFFI1218OSBH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0010963/",
"term_name": "Illumina NextSeq 2000"
},
"submitted_file_name": "/net/shendure/vol8/projects/JBL/GEO_sc_rep_fastqs_nobackup/geo_submission_20221108/bulkMPRA_devCRE_mEBs/bulk_MPRA_mEB_series_mBC_repA_d18_RNA_R3_001.fastq.gz",
"upload_status": "validated"
}
],
"input_file_set_for": [
"/analysis-sets/IGVFDS2622CKLA/"
],
"lab": {
"@id": "/labs/jay-shendure/",
"title": "Jay Shendure, UW"
},
"notes": "The readout b59a5259-3a53-482b-a7a5-6f401bdad220 was removed from this measurement set.",
"preferred_assay_title": "MPRA",
"protocols": [
"https://www.protocols.io/file/n92rb7r27.pdf"
],
"publications": [
{
"@id": "/publications/398edd7f-1ebb-40a0-a04b-450a2565667c/",
"publication_identifiers": [
"doi:10.1038/s41592-024-02260-3",
"PMID:38724692"
]
}
],
"release_timestamp": "2024-06-27T00:41:16.780700+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM1019NMFD/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1019NMFD",
"aliases": [
"jay-shendure:dev_CRE_mEBs_repA_bulk_day18"
],
"cell_fate_change_treatments": [
{
"@id": "/treatments/9acc7857-c9dd-4b4a-a78b-fdf10c8ae679/",
"purpose": "differentiation",
"summary": "Depletion of Leukemia inhibitory factor",
"treatment_type": "protein"
}
],
"classifications": [
"differentiated cell specimen"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS7655GRFI/",
"accession": "IGVFDS7655GRFI",
"file_set_type": "reporter library",
"summary": "Reporter library targeting accessible genome regions in many genomic loci"
}
],
"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 18 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": "21",
"status": "released",
"submitted_by": {
"@id": "/users/73f58e9f-8f5d-4fee-a7cd-dd63c0167e4b/",
"title": "Beth Martin"
},
"submitted_files_timestamp": "2023-12-09T00:55:22.517358+00:00",
"summary": "MPRA integrating a reporter library targeting accessible genome regions in many genomic loci",
"uuid": "d06c9bc1-8602-49f2-99ba-0dee0a8166e4"
}