{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1680VACI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1680VACI",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set9"
],
"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 [IGVFDS1680VACI](/measurement-sets/IGVFDS1680VACI/) 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/IGVFDS1680VACI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1680VACI](/measurement-sets/IGVFDS1680VACI/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1680VACI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1680VACI](/measurement-sets/IGVFDS1680VACI/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1680VACI/"
},
{
"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 [IGVFDS1680VACI](/measurement-sets/IGVFDS1680VACI/) 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/IGVFDS1680VACI/"
}
],
"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": "2025-02-07T01:58:07.932541+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/IGVFDO6000ECIY/",
"accession": "IGVFDO6000ECIY",
"aliases": [
"buenrostro-bernstein:surya-DSS16-DSS-m2"
],
"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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI1513HTOS/",
"accession": "IGVFFI1513HTOS",
"aliases": [
"buenrostro-bernstein:IGVFFI2327DFZG_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:54:03.387494+00:00",
"file_format": "yaml",
"file_size": 1220,
"href": "/configuration-files/IGVFFI1513HTOS/@@download/IGVFFI1513HTOS.yaml.gz",
"md5sum": "4d2bbaee6e37a558d9ed399cb9fcbe04",
"s3_uri": "s3://igvf-files/2025/03/18/ed282649-c44d-463d-921d-c267d0dc852e/IGVFFI1513HTOS.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI2327DFZG_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7719OGVL/",
"accession": "IGVFFI7719OGVL",
"aliases": [
"buenrostro-bernstein:surya-DSS16-prim-9K-1-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:53.337149+00:00",
"file_format": "fastq",
"file_size": 4422843140,
"href": "/sequence-files/IGVFFI7719OGVL/@@download/IGVFFI7719OGVL.fastq.gz",
"md5sum": "50788a08512d9044ac3066dbc6efdf0a",
"s3_uri": "s3://igvf-files/2025/02/07/90d80fdf-2cbc-4178-bf67-283db7edbb17/IGVFFI7719OGVL.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-1-ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2327DFZG/",
"accession": "IGVFFI2327DFZG",
"aliases": [
"buenrostro-bernstein:surya-DSS16-prim-9K-1-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:07.591870+00:00",
"file_format": "fastq",
"file_size": 4092342307,
"href": "/sequence-files/IGVFFI2327DFZG/@@download/IGVFFI2327DFZG.fastq.gz",
"md5sum": "45cca4da052a48e88fdb8203677390a6",
"s3_uri": "s3://igvf-files/2025/02/07/07037eea-03e9-4564-980b-23bcb374ce59/IGVFFI2327DFZG.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-1-ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6721AYTQ/",
"accession": "IGVFFI6721AYTQ",
"aliases": [
"buenrostro-bernstein:surya-DSS16-prim-9K-1-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:50:04.233336+00:00",
"file_format": "fastq",
"file_size": 1366843872,
"href": "/sequence-files/IGVFFI6721AYTQ/@@download/IGVFFI6721AYTQ.fastq.gz",
"md5sum": "108357368d635f3528fc02c7e189e60c",
"s3_uri": "s3://igvf-files/2025/03/14/fd276851-9734-4073-9ee6-3033ca646b69/IGVFFI6721AYTQ.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-1-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/IGVFDS3212RENM/",
"accession": "IGVFDS3212RENM",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4205JWPE/",
"accession": "IGVFDS4205JWPE",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1130NULC/",
"accession": "IGVFDS1130NULC",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:34:47.071768+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": "2025-02-07T01:59:07.591870+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "46f120e8-e751-4c8d-a585-716a40bf1780"
}