{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3212RENM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3212RENM",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set10"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3212RENM](/measurement-sets/IGVFDS3212RENM/) has no `publications`. Released and archived file sets are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_file_set_missing_publication",
"path": "/measurement-sets/IGVFDS3212RENM/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3212RENM](/measurement-sets/IGVFDS3212RENM/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3212RENM/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3212RENM](/measurement-sets/IGVFDS3212RENM/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3212RENM/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM7017UXAA](/primary-cells/IGVFSM7017UXAA/) has no `publications`. Released and archived samples are expected to be associated with a publication.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_sample_missing_publication",
"path": "/primary-cells/IGVFSM7017UXAA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3212RENM](/measurement-sets/IGVFDS3212RENM/) is missing required `strand_specificity`. Single-cell assays are expected to specify strand specificity.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_strand_specificity",
"path": "/measurement-sets/IGVFDS3212RENM/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM7017UXAA](/primary-cells/IGVFSM7017UXAA/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
"level": 40,
"level_name": "WARNING",
"name": "audit_biosample_age",
"path": "/primary-cells/IGVFSM7017UXAA/"
}
]
},
"award": {
"@id": "/awards/HG011986/",
"component": "mapping",
"contact_pi": {
"@id": "/users/33c6eb70-e143-4f77-9661-4b3905737daa/",
"title": "Jason Buenrostro"
},
"title": "A foundational resource of functional elements, TF footprints and gene regulatory interactions"
},
"control_for": [],
"creation_timestamp": "2025-02-07T01:58:05.151673+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"description": "Colitis_recovered DSS16-DSS-m1,DSS16-DSS-m2; Control DSS16-Control-m3",
"donors": [
{
"@id": "/rodent-donors/IGVFDO5001DPQO/",
"accession": "IGVFDO5001DPQO",
"aliases": [
"buenrostro-bernstein:surya-DSS16-Control-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO2984VHVD/",
"accession": "IGVFDO2984VHVD",
"aliases": [
"buenrostro-bernstein:surya-DSS16-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6000ECIY/",
"accession": "IGVFDO6000ECIY",
"aliases": [
"buenrostro-bernstein:surya-DSS16-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI2836UUTC/",
"accession": "IGVFFI2836UUTC",
"aliases": [
"buenrostro-bernstein:IGVFFI5303RQBI_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:53:49.354851+00:00",
"file_format": "yaml",
"file_size": 1219,
"href": "/configuration-files/IGVFFI2836UUTC/@@download/IGVFFI2836UUTC.yaml.gz",
"md5sum": "7483b1b9bf730c078495d91a22677236",
"s3_uri": "s3://igvf-files/2025/03/18/4c12f995-d35b-40c4-aee8-054f25461fa8/IGVFFI2836UUTC.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI5303RQBI_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5303RQBI/",
"accession": "IGVFFI5303RQBI",
"aliases": [
"buenrostro-bernstein:surya-DSS16-prim-9K-2-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:09.469024+00:00",
"file_format": "fastq",
"file_size": 4698692722,
"href": "/sequence-files/IGVFFI5303RQBI/@@download/IGVFFI5303RQBI.fastq.gz",
"md5sum": "65f689958389a66188c89cfdccc906e3",
"s3_uri": "s3://igvf-files/2025/02/07/fcd01b7a-76b4-4068-9550-4442e2d61872/IGVFFI5303RQBI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/DSS16-prim-9K-2-ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0162FERT/",
"accession": "IGVFFI0162FERT",
"aliases": [
"buenrostro-bernstein:surya-DSS16-prim-9K-2-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:54.720620+00:00",
"file_format": "fastq",
"file_size": 5032753041,
"href": "/sequence-files/IGVFFI0162FERT/@@download/IGVFFI0162FERT.fastq.gz",
"md5sum": "143dec9020e34be0f9ad43c134952468",
"s3_uri": "s3://igvf-files/2025/02/07/f6ac5b5e-c317-469b-a8fe-6190e4a173d0/IGVFFI0162FERT.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/DSS16-prim-9K-2-ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7946JZHZ/",
"accession": "IGVFFI7946JZHZ",
"aliases": [
"buenrostro-bernstein:surya-DSS16-prim-9K-2-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:50:10.038533+00:00",
"file_format": "fastq",
"file_size": 1540339438,
"href": "/sequence-files/IGVFFI7946JZHZ/@@download/IGVFFI7946JZHZ.fastq.gz",
"md5sum": "702039b499f8103d01d7af26b59b942b",
"s3_uri": "s3://igvf-files/2025/03/14/13ade145-d94f-4d68-9b8a-e574262e0db2/IGVFFI7946JZHZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/submit-fqs/barcode-file/DSS16-prim-9K-2-ATAC.barcode.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0237MRDL/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 4,
"onlist_files": [
"/tabular-files/IGVFFI4393VVCW/",
"/tabular-files/IGVFFI9683HRGJ/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-v1-6qpvrdexpgmk/v1"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS4205JWPE/",
"accession": "IGVFDS4205JWPE",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1130NULC/",
"accession": "IGVFDS1130NULC",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1680VACI/",
"accession": "IGVFDS1680VACI",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:34:32.235844+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM7017UXAA/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7017UXAA",
"aliases": [
"buenrostro-bernstein:surya-DSS16-DSS-m1 1_to_32, DSS16-DSS-m2 33_to_64, DSS16-Control-m3 65_to_96"
],
"classifications": [
"primary cell"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0001155/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "colon",
"term_name": "colon"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6J colon cell",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-02-07T01:59:09.469024+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "700156e2-cbab-4b4d-a1a5-407a8a7a1d58"
}