{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS6788EJWD/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS6788EJWD",
"aliases": [
"buenrostro-bernstein:scRNA Lib 813"
],
"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 [IGVFDS6788EJWD](/measurement-sets/IGVFDS6788EJWD/) 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/IGVFDS6788EJWD/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6788EJWD](/measurement-sets/IGVFDS6788EJWD/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6788EJWD/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS6788EJWD](/measurement-sets/IGVFDS6788EJWD/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS6788EJWD/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM3008DKJO](/tissues/IGVFSM3008DKJO/) 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/IGVFSM3008DKJO/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS6788EJWD](/measurement-sets/IGVFDS6788EJWD/) 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/IGVFDS6788EJWD/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM3008DKJO](/tissues/IGVFSM3008DKJO/) 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/IGVFSM3008DKJO/"
}
]
},
"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": "2025-03-05T15:34:36.574936+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/IGVFFI8489AOBV/",
"accession": "IGVFFI8489AOBV",
"aliases": [
"buenrostro-bernstein:SS-LS_8326_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:00.485055+00:00",
"file_format": "fastq",
"file_size": 4068817428,
"href": "/sequence-files/IGVFFI8489AOBV/@@download/IGVFFI8489AOBV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/358555f5-7525-4825-8c30-e0d720cc05b5/IGVFFI8489AOBV.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-2180_L7_SS-PKR-583_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1480BRSU/",
"accession": "IGVFFI1480BRSU",
"aliases": [
"buenrostro-bernstein:SS-LS_8326_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:04.217012+00:00",
"file_format": "fastq",
"file_size": 7092608197,
"href": "/sequence-files/IGVFFI1480BRSU/@@download/IGVFFI1480BRSU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a2d5af53-8eba-421e-9dc0-1a43dbbfdd53/IGVFFI1480BRSU.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-2180_L7_SS-PKR-583_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4993DPZN/",
"accession": "IGVFFI4993DPZN",
"aliases": [
"buenrostro-bernstein:SS-LS_8366_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:12.188719+00:00",
"file_format": "fastq",
"file_size": 2316442548,
"href": "/sequence-files/IGVFFI4993DPZN/@@download/IGVFFI4993DPZN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4c7fa1b4-83b6-4326-a159-d466efedeff9/IGVFFI4993DPZN.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-2220_L7_SS-PKR-583_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2640BUDC/",
"accession": "IGVFFI2640BUDC",
"aliases": [
"buenrostro-bernstein:SS-LS_8366_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:14.143432+00:00",
"file_format": "fastq",
"file_size": 3947904687,
"href": "/sequence-files/IGVFFI2640BUDC/@@download/IGVFFI2640BUDC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a3ca080e-1a9c-4151-9fd1-ed6293de1cce/IGVFFI2640BUDC.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-2220_L7_SS-PKR-583_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1256BVGX/",
"accession": "IGVFFI1256BVGX",
"aliases": [
"buenrostro-bernstein:SS-LS_8366_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:34.120643+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI1256BVGX/@@download/IGVFFI1256BVGX.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/38a6f95b-b965-4825-b8ba-fb81a46901f6/IGVFFI1256BVGX.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8366_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2565WUYM/",
"accession": "IGVFFI2565WUYM",
"aliases": [
"buenrostro-bernstein:SS-LS_8326_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:17.707269+00:00",
"file_format": "yaml",
"file_size": 1284,
"href": "/configuration-files/IGVFFI2565WUYM/@@download/IGVFFI2565WUYM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/42d6ce75-a9b5-44d3-a75c-1088e72bc011/IGVFFI2565WUYM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8326_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7295AVMP/"
],
"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/IGVFDS9037YGVR/",
"accession": "IGVFDS9037YGVR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:40.855028+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM3008DKJO/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3008DKJO",
"aliases": [
"buenrostro-bernstein:BioSam 5149_SS-PKR 583"
],
"cellular_sub_pool": "SS-PKR 583",
"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 583)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:58:00.485055+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "3e790082-a012-4459-a432-e3b9b1b1f08b"
}