{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3861CXLU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3861CXLU",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set5"
],
"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 [IGVFDS3861CXLU](/measurement-sets/IGVFDS3861CXLU/) 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/IGVFDS3861CXLU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3861CXLU](/measurement-sets/IGVFDS3861CXLU/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3861CXLU/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3861CXLU](/measurement-sets/IGVFDS3861CXLU/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3861CXLU/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM0354RWOF](/primary-cells/IGVFSM0354RWOF/) 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/IGVFSM0354RWOF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3861CXLU](/measurement-sets/IGVFDS3861CXLU/) 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/IGVFDS3861CXLU/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0354RWOF](/primary-cells/IGVFSM0354RWOF/) 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/IGVFSM0354RWOF/"
}
]
},
"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": "2025-02-07T01:58:14.530162+00:00",
"description": "Colitis_chronic DSS05-DSS-m1,DSS05-DSS-m2; Control DSS05-Control-m3,DSS05-Control-m4",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9526OTLM/",
"accession": "IGVFDO9526OTLM",
"aliases": [
"buenrostro-bernstein:surya-DSS05-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4795UJTB/",
"accession": "IGVFDO4795UJTB",
"aliases": [
"buenrostro-bernstein:surya-DSS05-Control-m4"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0997UHAO/",
"accession": "IGVFDO0997UHAO",
"aliases": [
"buenrostro-bernstein:surya-DSS05-Control-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4865EMFK/",
"accession": "IGVFDO4865EMFK",
"aliases": [
"buenrostro-bernstein:surya-DSS05-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI7112FBEP/",
"accession": "IGVFFI7112FBEP",
"aliases": [
"buenrostro-bernstein:IGVFFI5103LWRW_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:53:58.006327+00:00",
"file_format": "yaml",
"file_size": 1212,
"href": "/configuration-files/IGVFFI7112FBEP/@@download/IGVFFI7112FBEP.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/8e6dba81-9701-4179-bf02-66388707474b/IGVFFI7112FBEP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI5103LWRW_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5103LWRW/",
"accession": "IGVFFI5103LWRW",
"aliases": [
"buenrostro-bernstein:surya-dss05_prim_12k_1_ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:01.104716+00:00",
"file_format": "fastq",
"file_size": 3062302150,
"href": "/sequence-files/IGVFFI5103LWRW/@@download/IGVFFI5103LWRW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/8c3d4039-4ae1-43ac-b987-08f3ca5805c0/IGVFFI5103LWRW.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/dss05_prim_12k_1_ATAC.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2541TDKG/",
"accession": "IGVFFI2541TDKG",
"aliases": [
"buenrostro-bernstein:surya-dss05_prim_12k_1_ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:47.505872+00:00",
"file_format": "fastq",
"file_size": 3153586737,
"href": "/sequence-files/IGVFFI2541TDKG/@@download/IGVFFI2541TDKG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/2134657b-f082-4f5d-9bcf-080947c024d1/IGVFFI2541TDKG.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/dss05_prim_12k_1_ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1885ZBYE/",
"accession": "IGVFFI1885ZBYE",
"aliases": [
"buenrostro-bernstein:surya-dss05_prim_12k_1_ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:42.354361+00:00",
"file_format": "fastq",
"file_size": 1586856861,
"href": "/sequence-files/IGVFFI1885ZBYE/@@download/IGVFFI1885ZBYE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/28777cb2-172a-4f42-8e5f-baf293a1c84c/IGVFFI1885ZBYE.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/dss05_prim_12k_1_ATAC.barcode.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0237MRDL/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 6,
"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/IGVFDS6690HJKJ/",
"accession": "IGVFDS6690HJKJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9364TNAM/",
"accession": "IGVFDS9364TNAM",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8684IGUT/",
"accession": "IGVFDS8684IGUT",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6729QWDJ/",
"accession": "IGVFDS6729QWDJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6298OKGJ/",
"accession": "IGVFDS6298OKGJ",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:34:04.651553+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM0354RWOF/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0354RWOF",
"aliases": [
"buenrostro-bernstein:surya-DSS05-DSS-m1 1_to_16, DSS05-DSS-m2 17_to_48, DSS05-Control-m3 49_to_80, DSS05-Control-m4 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": "2025-02-07T01:59:01.104716+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "618b222f-1d77-4314-959e-1e5ff3e4392f"
}