{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6417ZIEI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6417ZIEI",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set1"
],
"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 [IGVFDS6417ZIEI](/measurement-sets/IGVFDS6417ZIEI/) 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/IGVFDS6417ZIEI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6417ZIEI](/measurement-sets/IGVFDS6417ZIEI/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6417ZIEI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6417ZIEI](/measurement-sets/IGVFDS6417ZIEI/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6417ZIEI/"
},
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM0332KRWE](/primary-cells/IGVFSM0332KRWE/) 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/IGVFSM0332KRWE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6417ZIEI](/measurement-sets/IGVFDS6417ZIEI/) 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/IGVFDS6417ZIEI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM0332KRWE](/primary-cells/IGVFSM0332KRWE/) 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/IGVFSM0332KRWE/"
}
]
},
"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": "2025-02-07T01:58:01.160348+00:00",
"description": "Colitis_chronic DSS04-DSS-m1,DSS04-DSS-m2,DSS04-DSS-m3; Control DSS04-Control-m4,DSS04-Control-m5",
"donors": [
{
"@id": "/rodent-donors/IGVFDO4534AFBQ/",
"accession": "IGVFDO4534AFBQ",
"aliases": [
"buenrostro-bernstein:surya-DSS04-Control-m5"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4695LJXX/",
"accession": "IGVFDO4695LJXX",
"aliases": [
"buenrostro-bernstein:surya-DSS04-DSS-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO6702IDOE/",
"accession": "IGVFDO6702IDOE",
"aliases": [
"buenrostro-bernstein:surya-DSS04-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO1905EGPL/",
"accession": "IGVFDO1905EGPL",
"aliases": [
"buenrostro-bernstein:surya-DSS04-Control-m4"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO0874UTHD/",
"accession": "IGVFDO0874UTHD",
"aliases": [
"buenrostro-bernstein:surya-DSS04-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7960YELB/",
"accession": "IGVFFI7960YELB",
"aliases": [
"buenrostro-bernstein:surya-DSS04-prim-ATAC.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-18T15:33:58.777245+00:00",
"file_format": "fastq",
"file_size": 256873401,
"href": "/sequence-files/IGVFFI7960YELB/@@download/IGVFFI7960YELB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/18/cc8355a6-2095-48b4-899d-af2c420a8313/IGVFFI7960YELB.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/DSS04-prim-ATAC.barcode.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0542VGMW/",
"accession": "IGVFFI0542VGMW",
"aliases": [
"buenrostro-bernstein:IGVFFI9338UHLG_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:53:48.007951+00:00",
"file_format": "yaml",
"file_size": 1211,
"href": "/configuration-files/IGVFFI0542VGMW/@@download/IGVFFI0542VGMW.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/2f2af1b1-51be-4511-b1fa-4bda89328350/IGVFFI0542VGMW.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI9338UHLG_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9338UHLG/",
"accession": "IGVFFI9338UHLG",
"aliases": [
"buenrostro-bernstein:surya-DSS04-prim-ATAC.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:39.749448+00:00",
"file_format": "fastq",
"file_size": 520630542,
"href": "/sequence-files/IGVFFI9338UHLG/@@download/IGVFFI9338UHLG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/1ee45c07-c084-4a4c-bab5-38ce8586efdd/IGVFFI9338UHLG.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/DSS04-prim-ATAC.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3705PWOQ/",
"accession": "IGVFFI3705PWOQ",
"aliases": [
"buenrostro-bernstein:surya-DSS04-prim-ATAC.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:58:54.765878+00:00",
"file_format": "fastq",
"file_size": 501575612,
"href": "/sequence-files/IGVFFI3705PWOQ/@@download/IGVFFI3705PWOQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/fd1c6bbe-b323-4df8-86df-38a105f2e4be/IGVFFI3705PWOQ.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/DSS04-prim-ATAC.R1.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/IGVFDS5841CMLA/",
"accession": "IGVFDS5841CMLA",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1815DBIG/",
"accession": "IGVFDS1815DBIG",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5960BAQO/",
"accession": "IGVFDS5960BAQO",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS5627HIFZ/",
"accession": "IGVFDS5627HIFZ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6334KAGT/",
"accession": "IGVFDS6334KAGT",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:34:17.058529+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM0332KRWE/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM0332KRWE",
"aliases": [
"buenrostro-bernstein:surya-DSS04-DSS-m1 1_to_16, DSS04-DSS-m2 17_to_32, DSS04-DSS-m3 33_to_56, DSS04-Control-m4 57_to_76, DSS04-Control-m5 77_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": "2025-02-07T01:58:54.765878+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "ce92a1fe-02c1-4f43-acdf-404001b186df"
}