{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7875RFFR/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7875RFFR",
"aliases": [
"charles-gersbach:measurement-set-bulk-atac-control-ipsc-cm-rep2"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003089/",
"status": "released",
"term_name": "bulk assay for transposase-accessible chromatin using sequencing"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7875RFFR](/measurement-sets/IGVFDS7875RFFR/) has sequence file(s): [IGVFFI7818LEWI](/sequence-files/IGVFFI7818LEWI/), [IGVFFI2839CBYW](/sequence-files/IGVFFI2839CBYW/) 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": "/measurement-sets/IGVFDS7875RFFR/"
}
]
},
"award": {
"@id": "/awards/HG012053/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
"title": "Charles Gersbach"
},
"title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
},
"control_for": [
{
"@id": "/measurement-sets/IGVFDS9961QTUB/",
"accession": "IGVFDS9961QTUB",
"aliases": [
"charles-gersbach:measurement-set-bulk-atac-chir4um-ipsc-cm-rep2"
],
"status": "released"
}
],
"creation_timestamp": "2024-10-23T19:19:50.836583+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO3212TBUN/",
"accession": "IGVFDO3212TBUN",
"aliases": [
"charles-gersbach:human-donor-WTC11"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7818LEWI/",
"accession": "IGVFFI7818LEWI",
"aliases": [
"charles-gersbach:measurement-set-bulk-atac-control-ipsc-cm-rep2-R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:06.675682+00:00",
"file_format": "fastq",
"file_size": 1155710785,
"href": "/sequence-files/IGVFFI7818LEWI/@@download/IGVFFI7818LEWI.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/d9f56913-8ddd-4a88-a630-9541e02b543f/IGVFFI7818LEWI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/tda17/Anglen_7276_210923B6/data/atac_seq/processed_raw_reads/Anglen_7276_210923B6/Control_2.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2839CBYW/",
"accession": "IGVFFI2839CBYW",
"aliases": [
"charles-gersbach:measurement-set-bulk-atac-control-ipsc-cm-rep2-R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-10-23T19:29:05.397092+00:00",
"file_format": "fastq",
"file_size": 1184261147,
"href": "/sequence-files/IGVFFI2839CBYW/@@download/IGVFFI2839CBYW.fastq.gz",
"s3_uri": "s3://igvf-files/2024/10/23/58f03ebf-a618-4f30-947a-32c5f2b3ffe3/IGVFFI2839CBYW.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "/datacommons/gersbachlab/tda17/Anglen_7276_210923B6/data/atac_seq/processed_raw_reads/Anglen_7276_210923B6/Control_2.R1.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4606DSTJ/"
],
"lab": {
"@id": "/labs/charles-gersbach/",
"title": "Charles Gersbach, Duke"
},
"preferred_assay_title": "ATAC-seq",
"protocols": [
"https://www.protocols.io/view/atac-seq-for-human-ipsc-cm-following-gsk3-inhibiti-5qpvokj27l4o"
],
"release_timestamp": "2024-12-03T20:43:50.890076+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM7187NNQU/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7187NNQU",
"aliases": [
"charles-gersbach:in-vitro-system-bulk-atac-control-ipsc-cm-rep2"
],
"classifications": [
"differentiated cell specimen"
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0009747/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:WTC11"
],
"status": "released",
"summary": "GM25256 (WTC-11)",
"term_name": "GM25256 (WTC-11)"
}
],
"status": "released",
"summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
"targeted_sample_term": {
"@id": "/sample-terms/CL_0000746/",
"status": "released",
"term_name": "cardiac muscle cell"
},
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "released",
"submitted_by": {
"@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
"title": "Ruhi Rai"
},
"submitted_files_timestamp": "2024-10-23T19:29:05.397092+00:00",
"summary": "ATAC-seq",
"uuid": "c77f414c-eb99-46ac-90bd-f4ed6cb67f31"
}