{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0997DPPP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0997DPPP",
"aliases": [
"buenrostro-bernstein:scRNA Lib 809"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002631/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-cell RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "NTR term ID",
"detail": "Sample term for [NTR_0000646](/sample-terms/NTR_0000646/) has been newly requested. Ontology terms with a newly requested term ID are expected to have it updated following its addition to the appropriate ontology database.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_ntr_term_id",
"path": "/sample-terms/NTR_0000646/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS0997DPPP](/measurement-sets/IGVFDS0997DPPP/) 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/IGVFDS0997DPPP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0997DPPP](/measurement-sets/IGVFDS0997DPPP/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0997DPPP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0997DPPP](/measurement-sets/IGVFDS0997DPPP/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0997DPPP/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM7444XSMN](/tissues/IGVFSM7444XSMN/) 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": "/tissues/IGVFSM7444XSMN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0997DPPP](/measurement-sets/IGVFDS0997DPPP/) 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/IGVFDS0997DPPP/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM7444XSMN](/tissues/IGVFSM7444XSMN/) 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": "/tissues/IGVFSM7444XSMN/"
}
]
},
"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": "2025-03-05T15:34:33.153512+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO7272VQKZ/",
"accession": "IGVFDO7272VQKZ",
"aliases": [
"ali-mortazavi:770_CASTJ_10F",
"buenrostro-bernstein:Donor 2072"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4880UJBC/",
"accession": "IGVFFI4880UJBC",
"aliases": [
"buenrostro-bernstein:SS-LS_8322_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:53.819182+00:00",
"file_format": "fastq",
"file_size": 5832538523,
"href": "/sequence-files/IGVFFI4880UJBC/@@download/IGVFFI4880UJBC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d993fac9-3acd-442f-b66c-36b4b3d13030/IGVFFI4880UJBC.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2176_L7_SS-PKR-574_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7030TJKX/",
"accession": "IGVFFI7030TJKX",
"aliases": [
"buenrostro-bernstein:SS-LS_8362_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:00.860750+00:00",
"file_format": "fastq",
"file_size": 1915723948,
"href": "/sequence-files/IGVFFI7030TJKX/@@download/IGVFFI7030TJKX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4d34917b-74ce-4237-90c8-aa316514d4dc/IGVFFI7030TJKX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2216_L7_SS-PKR-574_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1904WOQS/",
"accession": "IGVFFI1904WOQS",
"aliases": [
"buenrostro-bernstein:SS-LS_8362_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:02.799827+00:00",
"file_format": "fastq",
"file_size": 3274571614,
"href": "/sequence-files/IGVFFI1904WOQS/@@download/IGVFFI1904WOQS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/68f1785e-8311-43e5-b5fe-4b5f41519569/IGVFFI1904WOQS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2216_L7_SS-PKR-574_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4650CEAX/",
"accession": "IGVFFI4650CEAX",
"aliases": [
"buenrostro-bernstein:SS-LS_8322_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:51.745270+00:00",
"file_format": "fastq",
"file_size": 3348342186,
"href": "/sequence-files/IGVFFI4650CEAX/@@download/IGVFFI4650CEAX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/07d4bf3a-a153-4cfb-8a51-420ac8d14040/IGVFFI4650CEAX.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0022840/",
"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2176_L7_SS-PKR-574_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0103KUWP/",
"accession": "IGVFFI0103KUWP",
"aliases": [
"buenrostro-bernstein:SS-LS_8362_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:30.325203+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI0103KUWP/@@download/IGVFFI0103KUWP.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/2b7ea307-5e7d-4126-9eac-024e2c0a6790/IGVFFI0103KUWP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8362_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2329SMGD/",
"accession": "IGVFFI2329SMGD",
"aliases": [
"buenrostro-bernstein:SS-LS_8322_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:13.349746+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI2329SMGD/@@download/IGVFFI2329SMGD.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/be9c2376-102f-4331-b906-8ce28462cd62/IGVFFI2329SMGD.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8322_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9358DHKB/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/tabular-files/IGVFFI2668ZFEB/"
],
"onlist_method": "multi",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS6623PZMD/",
"accession": "IGVFDS6623PZMD",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:51.034820+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM7444XSMN/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7444XSMN",
"aliases": [
"buenrostro-bernstein:BioSam 5149_SS-PKR 574"
],
"cellular_sub_pool": "SS-PKR 574",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/NTR_0000646/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "left cerebral cortex",
"term_name": "left cerebral cortex"
}
],
"status": "released",
"summary": "Mus musculus CAST/EiJ (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 574)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:51.745270+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "e4d1f018-0f79-4487-8d8d-5a773016b6b6"
}