{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3505NISC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3505NISC",
"aliases": [
"buenrostro-bernstein:scRNA Lib 810"
],
"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": "Tissue [IGVFSM5470EUSZ](/tissues/IGVFSM5470EUSZ/) 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/IGVFSM5470EUSZ/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS3505NISC](/measurement-sets/IGVFDS3505NISC/) 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/IGVFDS3505NISC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3505NISC](/measurement-sets/IGVFDS3505NISC/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3505NISC/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3505NISC](/measurement-sets/IGVFDS3505NISC/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3505NISC/"
},
{
"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 [IGVFDS3505NISC](/measurement-sets/IGVFDS3505NISC/) 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/IGVFDS3505NISC/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM5470EUSZ](/tissues/IGVFSM5470EUSZ/) 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/IGVFSM5470EUSZ/"
}
]
},
"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": "2025-03-05T17:52:40.665221+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/IGVFFI5610AKBM/",
"accession": "IGVFFI5610AKBM",
"aliases": [
"buenrostro-bernstein:SS-LS_8323_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:39.645675+00:00",
"file_format": "fastq",
"file_size": 8082462945,
"href": "/sequence-files/IGVFFI5610AKBM/@@download/IGVFFI5610AKBM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f8ee90eb-bf0e-4994-8b78-509915738643/IGVFFI5610AKBM.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-2177_L7_SS-PKR-576_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7711ZQWS/",
"accession": "IGVFFI7711ZQWS",
"aliases": [
"buenrostro-bernstein:SS-LS_8323_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:38.237490+00:00",
"file_format": "fastq",
"file_size": 4716436239,
"href": "/sequence-files/IGVFFI7711ZQWS/@@download/IGVFFI7711ZQWS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/c0bc0678-e481-4c40-bd27-a23a891a2bf7/IGVFFI7711ZQWS.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-2177_L7_SS-PKR-576_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8934BYBA/",
"accession": "IGVFFI8934BYBA",
"aliases": [
"buenrostro-bernstein:SS-LS_8363_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:08.706516+00:00",
"file_format": "fastq",
"file_size": 2511490743,
"href": "/sequence-files/IGVFFI8934BYBA/@@download/IGVFFI8934BYBA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5be4c9f2-38cc-458a-aa73-3659d142ad8a/IGVFFI8934BYBA.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-2217_L7_SS-PKR-576_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5005GVTP/",
"accession": "IGVFFI5005GVTP",
"aliases": [
"buenrostro-bernstein:SS-LS_8363_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:10.078513+00:00",
"file_format": "fastq",
"file_size": 4323828950,
"href": "/sequence-files/IGVFFI5005GVTP/@@download/IGVFFI5005GVTP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/cb1426b2-8a28-47c3-9855-6f7cbf1125c1/IGVFFI5005GVTP.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-2217_L7_SS-PKR-576_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3555QFTM/",
"accession": "IGVFFI3555QFTM",
"aliases": [
"buenrostro-bernstein:SS-LS_8363_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:14.852570+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI3555QFTM/@@download/IGVFFI3555QFTM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/2f42d29a-33f3-4f43-836b-f39bb317f24c/IGVFFI3555QFTM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8363_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7835GATM/",
"accession": "IGVFFI7835GATM",
"aliases": [
"buenrostro-bernstein:SS-LS_8323_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:56:58.559473+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI7835GATM/@@download/IGVFFI7835GATM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/67c7c1ac-4910-4a12-9a36-4008f4e2523b/IGVFFI7835GATM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8323_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8031DVEU/"
],
"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/IGVFDS1861QPYY/",
"accession": "IGVFDS1861QPYY",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:58.337712+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM5470EUSZ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5470EUSZ",
"aliases": [
"buenrostro-bernstein:BioSam 5154_SS-PKR 576"
],
"cellular_sub_pool": "SS-PKR 576",
"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 576)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T17:57:38.237490+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "b20bb257-c342-4237-8a05-062e4de7a25e"
}