{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5841CMLA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5841CMLA",
"aliases": [
"buenrostro-bernstein:surya-mouse-colon_mm-set14"
],
"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": "Measurement set [IGVFDS5841CMLA](/measurement-sets/IGVFDS5841CMLA/) 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/IGVFDS5841CMLA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5841CMLA](/measurement-sets/IGVFDS5841CMLA/) has in progress subobject tabular file [IGVFFI9683HRGJ](/tabular-files/IGVFFI9683HRGJ/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5841CMLA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5841CMLA](/measurement-sets/IGVFDS5841CMLA/) has in progress subobject tabular file [IGVFFI4393VVCW](/tabular-files/IGVFFI4393VVCW/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5841CMLA/"
},
{
"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 [IGVFDS5841CMLA](/measurement-sets/IGVFDS5841CMLA/) 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/IGVFDS5841CMLA/"
}
],
"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": "2025-02-07T01:57:55.311314+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/IGVFDO6702IDOE/",
"accession": "IGVFDO6702IDOE",
"aliases": [
"buenrostro-bernstein:surya-DSS04-DSS-m2"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
},
{
"@id": "/rodent-donors/IGVFDO4534AFBQ/",
"accession": "IGVFDO4534AFBQ",
"aliases": [
"buenrostro-bernstein:surya-DSS04-Control-m5"
],
"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"
},
{
"@id": "/rodent-donors/IGVFDO1905EGPL/",
"accession": "IGVFDO1905EGPL",
"aliases": [
"buenrostro-bernstein:surya-DSS04-Control-m4"
],
"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"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/configuration-files/IGVFFI4296ZJRS/",
"accession": "IGVFFI4296ZJRS",
"aliases": [
"buenrostro-bernstein:IGVFFI9904OBDT_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-18T17:54:18.667788+00:00",
"file_format": "yaml",
"file_size": 1242,
"href": "/configuration-files/IGVFFI4296ZJRS/@@download/IGVFFI4296ZJRS.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/18/44254e32-b707-48e8-a37a-81a892e89d53/IGVFFI4296ZJRS.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/surya-mouse-colitis/seqspecs/IGVFFI9904OBDT_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9904OBDT/",
"accession": "IGVFFI9904OBDT",
"aliases": [
"buenrostro-bernstein:surya-DSS04-prim3-RNA.R2.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T02:00:00.714054+00:00",
"file_format": "fastq",
"file_size": 4117633998,
"href": "/sequence-files/IGVFFI9904OBDT/@@download/IGVFFI9904OBDT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/1736b674-add7-4bec-ab67-fdd4adfcb5ba/IGVFFI9904OBDT.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-prim3-RNA.R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1895BUYA/",
"accession": "IGVFFI1895BUYA",
"aliases": [
"buenrostro-bernstein:surya-DSS04-prim3-RNA.R1.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-02-07T01:59:21.034403+00:00",
"file_format": "fastq",
"file_size": 4212773114,
"href": "/sequence-files/IGVFFI1895BUYA/@@download/IGVFFI1895BUYA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/02/07/b556ae9d-64b9-4542-aac5-4d0762b160fd/IGVFFI1895BUYA.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-prim3-RNA.R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3920VHRX/",
"accession": "IGVFFI3920VHRX",
"aliases": [
"buenrostro-bernstein:surya-DSS04-prim3-RNA.barcode.fastq.gz"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-14T15:49:40.363328+00:00",
"file_format": "fastq",
"file_size": 2928977570,
"href": "/sequence-files/IGVFFI3920VHRX/@@download/IGVFFI3920VHRX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/14/42a7c432-b4f6-4e06-9f8a-52f43b3f555d/IGVFFI3920VHRX.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-prim3-RNA.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/IGVFDS1815DBIG/",
"accession": "IGVFDS1815DBIG",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS6417ZIEI/",
"accession": "IGVFDS6417ZIEI",
"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": "2025-03-26T17:34:23.593684+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": "2025-02-07T01:59:21.034403+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "35cd7444-ca13-4ba7-a1d5-c47e57c16dc7"
}