{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0463BASV/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0463BASV",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set8"
],
"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": "Primary cell [IGVFSM4720VFLQ](/primary-cells/IGVFSM4720VFLQ/) 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/IGVFSM4720VFLQ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0463BASV](/measurement-sets/IGVFDS0463BASV/) 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/IGVFDS0463BASV/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0463BASV](/measurement-sets/IGVFDS0463BASV/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0463BASV/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0463BASV](/measurement-sets/IGVFDS0463BASV/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0463BASV/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0463BASV](/measurement-sets/IGVFDS0463BASV/) 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/IGVFDS0463BASV/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM4720VFLQ](/primary-cells/IGVFSM4720VFLQ/) 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/IGVFSM4720VFLQ/"
}
]
},
"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": "2025-02-07T01:57:57.470422+00:00",
"description": "Colitis_recovered DSS15-DSS-m1,DSS15-DSS-m2,DSS15-DSS-m4; Control DSS15-Control-m3,DSS15-Control-m5",
"donors": [
{
"@id": "/rodent-donors/IGVFDO0860UBPI/",
"accession": "IGVFDO0860UBPI",
"aliases": [
"buenrostro-bernstein:surya-DSS15-Control-m5"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0902NXCE/",
"accession": "IGVFDO0902NXCE",
"aliases": [
"buenrostro-bernstein:surya-DSS15-DSS-m4"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO5812DIRC/",
"accession": "IGVFDO5812DIRC",
"aliases": [
"buenrostro-bernstein:surya-DSS15-Control-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO3340XHFP/",
"accession": "IGVFDO3340XHFP",
"aliases": [
"buenrostro-bernstein:surya-DSS15-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO8998VZHS/",
"accession": "IGVFDO8998VZHS",
"aliases": [
"buenrostro-bernstein:surya-DSS15-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI1964WNTJ/",
"accession": "IGVFFI1964WNTJ",
"aliases": [
"buenrostro-bernstein:IGVFFI1018OOCL_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:54:02.174811+00:00",
"file_format": "yaml",
"file_size": 1218,
"href": "/configuration-files/IGVFFI1964WNTJ/@@download/IGVFFI1964WNTJ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/8657b30a-9426-4d34-9a67-8ff248d7c15e/IGVFFI1964WNTJ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI1018OOCL_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1018OOCL/",
"accession": "IGVFFI1018OOCL",
"aliases": [
"buenrostro-bernstein:surya-DSS15-prim-20K-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:06.141685+00:00",
"file_format": "fastq",
"file_size": 10518321654,
"href": "/sequence-files/IGVFFI1018OOCL/@@download/IGVFFI1018OOCL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/3a76b072-0a42-4489-ac41-07d78f8ac7e6/IGVFFI1018OOCL.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/DSS15-prim-20K-ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0054RGNX/",
"accession": "IGVFFI0054RGNX",
"aliases": [
"buenrostro-bernstein:surya-DSS15-prim-20K-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:51.763270+00:00",
"file_format": "fastq",
"file_size": 11301334883,
"href": "/sequence-files/IGVFFI0054RGNX/@@download/IGVFFI0054RGNX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/d298f3ef-9001-49e2-a6d9-0c7371d54fd0/IGVFFI0054RGNX.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/DSS15-prim-20K-ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3924LWOL/",
"accession": "IGVFFI3924LWOL",
"aliases": [
"buenrostro-bernstein:surya-DSS15-prim-20K-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:54.865149+00:00",
"file_format": "fastq",
"file_size": 3518206233,
"href": "/sequence-files/IGVFFI3924LWOL/@@download/IGVFFI3924LWOL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/7050a9b0-4308-49c7-ac2f-0e3331c96e9f/IGVFFI3924LWOL.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/DSS15-prim-20K-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/IGVFDS1670HEIT/",
"accession": "IGVFDS1670HEIT",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9711DZFS/",
"accession": "IGVFDS9711DZFS",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3890CXMU/",
"accession": "IGVFDS3890CXMU",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:34:43.109230+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM4720VFLQ/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4720VFLQ",
"aliases": [
"buenrostro-bernstein:surya-DSS15-DSS-m1 1_to_16, DSS15-DSS-m2 17_to_32, DSS15-DSS-m4 33_to_48, DSS15-Control-m3 49_to_80, DSS15-Control-m5 81_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": "2025-02-07T01:59:06.141685+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "bee026a7-6e5d-457d-9c48-5e802cfa5f7c"
}