{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0131VONY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0131VONY",
"aliases": [
"buenrostro-bernstein:scRNA Lib 814"
],
"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 [IGVFDS0131VONY](/measurement-sets/IGVFDS0131VONY/) 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/IGVFDS0131VONY/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0131VONY](/measurement-sets/IGVFDS0131VONY/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0131VONY/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0131VONY](/measurement-sets/IGVFDS0131VONY/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0131VONY/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM6228EUYU](/tissues/IGVFSM6228EUYU/) 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/IGVFSM6228EUYU/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0131VONY](/measurement-sets/IGVFDS0131VONY/) 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/IGVFDS0131VONY/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6228EUYU](/tissues/IGVFSM6228EUYU/) 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/IGVFSM6228EUYU/"
}
]
},
"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": "2025-03-05T17:52:43.010381+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO4657FUEV/",
"accession": "IGVFDO4657FUEV",
"aliases": [
"ali-mortazavi:771_B6J_10M",
"buenrostro-bernstein:Donor 2077"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI6999CWFM/",
"accession": "IGVFFI6999CWFM",
"aliases": [
"buenrostro-bernstein:SS-LS_8367_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:15.785138+00:00",
"file_format": "fastq",
"file_size": 5883604525,
"href": "/sequence-files/IGVFFI6999CWFM/@@download/IGVFFI6999CWFM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4850e4ab-101b-4ebf-a17d-d96832909f17/IGVFFI6999CWFM.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-2221_L7_SS-PKR-584_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9321LTJT/",
"accession": "IGVFFI9321LTJT",
"aliases": [
"buenrostro-bernstein:SS-LS_8327_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:47.312707+00:00",
"file_format": "fastq",
"file_size": 10499777613,
"href": "/sequence-files/IGVFFI9321LTJT/@@download/IGVFFI9321LTJT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d6bc4503-3905-4f0b-9fa9-ce65eabdb2ad/IGVFFI9321LTJT.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-2181_L7_SS-PKR-584_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1583ELIM/",
"accession": "IGVFFI1583ELIM",
"aliases": [
"buenrostro-bernstein:SS-LS_8327_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:45.871230+00:00",
"file_format": "fastq",
"file_size": 6116718342,
"href": "/sequence-files/IGVFFI1583ELIM/@@download/IGVFFI1583ELIM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d4c0873f-8dca-4ade-b985-652c92f7ed66/IGVFFI1583ELIM.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-2181_L7_SS-PKR-584_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7119KXLF/",
"accession": "IGVFFI7119KXLF",
"aliases": [
"buenrostro-bernstein:SS-LS_8367_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:14.427150+00:00",
"file_format": "fastq",
"file_size": 3473066720,
"href": "/sequence-files/IGVFFI7119KXLF/@@download/IGVFFI7119KXLF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/7c0a75f6-cb94-4fbd-a8fe-44b61dbbae63/IGVFFI7119KXLF.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-2221_L7_SS-PKR-584_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8276VJEZ/",
"accession": "IGVFFI8276VJEZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8367_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:18.978420+00:00",
"file_format": "yaml",
"file_size": 1291,
"href": "/configuration-files/IGVFFI8276VJEZ/@@download/IGVFFI8276VJEZ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/72666c7a-dcfe-4eb6-8113-3b322b622cf8/IGVFFI8276VJEZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8367_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1639KWHH/",
"accession": "IGVFFI1639KWHH",
"aliases": [
"buenrostro-bernstein:SS-LS_8327_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:03.038376+00:00",
"file_format": "yaml",
"file_size": 1291,
"href": "/configuration-files/IGVFFI1639KWHH/@@download/IGVFFI1639KWHH.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/db2b1be6-1e1b-4b2b-81fa-5e4eeeadc0bd/IGVFFI1639KWHH.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8327_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4904NBTM/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI3897QKNI/",
"/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/IGVFDS4736GQFE/",
"accession": "IGVFDS4736GQFE",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:15.579484+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6228EUYU/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6228EUYU",
"aliases": [
"buenrostro-bernstein:BioSam 5154_SS-PKR 584"
],
"cellular_sub_pool": "SS-PKR 584",
"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 B6J (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 584)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T17:57:45.871230+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "645e4ff2-dd59-4bb5-8a13-73d47f77721f"
}