{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4279AZHG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4279AZHG",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set24"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing publication",
"detail": "Primary cell [IGVFSM1242TZJM](/primary-cells/IGVFSM1242TZJM/) 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/IGVFSM1242TZJM/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4279AZHG](/measurement-sets/IGVFDS4279AZHG/) 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/IGVFDS4279AZHG/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4279AZHG](/measurement-sets/IGVFDS4279AZHG/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4279AZHG/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4279AZHG](/measurement-sets/IGVFDS4279AZHG/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4279AZHG/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4279AZHG](/measurement-sets/IGVFDS4279AZHG/) 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/IGVFDS4279AZHG/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Primary cell [IGVFSM1242TZJM](/primary-cells/IGVFSM1242TZJM/) 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/IGVFSM1242TZJM/"
}
]
},
"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": "2025-02-07T01:57:54.066870+00:00",
"description": "Colitis_acute DSS17-DSS-m1,DSS17-DSS-m2,DSS18-DSS-m1,DSS18-DSS-m2; Control DSS17-Control-m3,DSS18-Control-m3",
"donors": [
{
"@id": "/rodent-donors/IGVFDO1782CWBW/",
"accession": "IGVFDO1782CWBW",
"aliases": [
"buenrostro-bernstein:surya-DSS18-Control-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO9911FTUN/",
"accession": "IGVFDO9911FTUN",
"aliases": [
"buenrostro-bernstein:surya-DSS18-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4820BFGB/",
"accession": "IGVFDO4820BFGB",
"aliases": [
"buenrostro-bernstein:surya-DSS18-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO9324UYNE/",
"accession": "IGVFDO9324UYNE",
"aliases": [
"buenrostro-bernstein:surya-DSS17-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO7063RDKN/",
"accession": "IGVFDO7063RDKN",
"aliases": [
"buenrostro-bernstein:surya-DSS17-Control-m3"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO3717FOSD/",
"accession": "IGVFDO3717FOSD",
"aliases": [
"buenrostro-bernstein:surya-DSS17-DSS-m1"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI3955OPFK/",
"accession": "IGVFFI3955OPFK",
"aliases": [
"buenrostro-bernstein:IGVFFI8335OFAN_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:54:33.008729+00:00",
"file_format": "yaml",
"file_size": 1241,
"href": "/configuration-files/IGVFFI3955OPFK/@@download/IGVFFI3955OPFK.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/9e2b76ac-9f7c-40d2-9ff2-d27f12d8757c/IGVFFI3955OPFK.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI8335OFAN_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6843NEUV/",
"accession": "IGVFFI6843NEUV",
"aliases": [
"buenrostro-bernstein:surya-DSS17-18-prim-2-RNA.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:00:17.217650+00:00",
"file_format": "fastq",
"file_size": 10906838924,
"href": "/sequence-files/IGVFFI6843NEUV/@@download/IGVFFI6843NEUV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/e346c72e-6a47-4b9b-9e37-369dc2a1b285/IGVFFI6843NEUV.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/DSS17-18-prim-2-RNA.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8335OFAN/",
"accession": "IGVFFI8335OFAN",
"aliases": [
"buenrostro-bernstein:surya-DSS17-18-prim-2-RNA.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:36.101588+00:00",
"file_format": "fastq",
"file_size": 9726945633,
"href": "/sequence-files/IGVFFI8335OFAN/@@download/IGVFFI8335OFAN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/6fce5d4e-7bbd-42bb-91fe-e620d51c8470/IGVFFI8335OFAN.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/DSS17-18-prim-2-RNA.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2649RUAJ/",
"accession": "IGVFFI2649RUAJ",
"aliases": [
"buenrostro-bernstein:surya-DSS17-18-prim-2-RNA.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:50:16.616433+00:00",
"file_format": "fastq",
"file_size": 3899757224,
"href": "/sequence-files/IGVFFI2649RUAJ/@@download/IGVFFI2649RUAJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/9d85ef03-60a6-495e-9988-36a59a0b9032/IGVFFI2649RUAJ.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/DSS17-18-prim-2-RNA.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/IGVFDS7425QRXB/",
"accession": "IGVFDS7425QRXB",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS9896MQFE/",
"accession": "IGVFDS9896MQFE",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8974KOJW/",
"accession": "IGVFDS8974KOJW",
"status": "released"
}
],
"release_timestamp": "2025-03-26T17:34:01.925316+00:00",
"samples": [
{
"@id": "/primary-cells/IGVFSM1242TZJM/",
"@type": [
"PrimaryCell",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1242TZJM",
"aliases": [
"buenrostro-bernstein:surya-DSS17-DSS-m1 1_to_16, DSS17-DSS-m2 17_to_32, DSS17-Control-m3 33_to_48, DSS18-DSS-m1 49_to_64, DSS18-DSS-m2 65_to_80, DSS18-Control-m3 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": "2025-02-07T01:59:36.101588+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "e22bd18b-b094-4584-8d46-3e54dd767a4b"
}