{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4886GWPA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4886GWPA",
"aliases": [
"buenrostro-bernstein:scRNA Lib 806"
],
"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": "Tissue [IGVFSM1072XOVT](/tissues/IGVFSM1072XOVT/) 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/IGVFSM1072XOVT/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS4886GWPA](/measurement-sets/IGVFDS4886GWPA/) 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/IGVFDS4886GWPA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4886GWPA](/measurement-sets/IGVFDS4886GWPA/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4886GWPA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4886GWPA](/measurement-sets/IGVFDS4886GWPA/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4886GWPA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4886GWPA](/measurement-sets/IGVFDS4886GWPA/) 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/IGVFDS4886GWPA/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1072XOVT](/tissues/IGVFSM1072XOVT/) 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/IGVFSM1072XOVT/"
}
]
},
"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": "2025-03-05T15:34:25.605770+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO2374RRPN/",
"accession": "IGVFDO2374RRPN",
"aliases": [
"ali-mortazavi:772_CASTJ_10F",
"buenrostro-bernstein:Donor 2074"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2872AMLA/",
"accession": "IGVFFI2872AMLA",
"aliases": [
"buenrostro-bernstein:SS-LS_8359_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:56.856403+00:00",
"file_format": "fastq",
"file_size": 1140501570,
"href": "/sequence-files/IGVFFI2872AMLA/@@download/IGVFFI2872AMLA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1ca57c73-4c48-4a3e-bfd0-2368341241b6/IGVFFI2872AMLA.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-2213_L7_SS-PKR-533_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6399EKWI/",
"accession": "IGVFFI6399EKWI",
"aliases": [
"buenrostro-bernstein:SS-LS_8303_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:27.162665+00:00",
"file_format": "fastq",
"file_size": 4767019861,
"href": "/sequence-files/IGVFFI6399EKWI/@@download/IGVFFI6399EKWI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/c7579956-ec31-47d3-95a9-caa2bb8b771b/IGVFFI6399EKWI.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-2173_L6_SS-PKR-533_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4017LTEF/",
"accession": "IGVFFI4017LTEF",
"aliases": [
"buenrostro-bernstein:SS-LS_8303_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:32.275124+00:00",
"file_format": "fastq",
"file_size": 8845286019,
"href": "/sequence-files/IGVFFI4017LTEF/@@download/IGVFFI4017LTEF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/408ac648-a232-40ca-aed2-093afeb13c60/IGVFFI4017LTEF.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-2173_L6_SS-PKR-533_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8664VYHD/",
"accession": "IGVFFI8664VYHD",
"aliases": [
"buenrostro-bernstein:SS-LS_8359_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:58.895348+00:00",
"file_format": "fastq",
"file_size": 1936856650,
"href": "/sequence-files/IGVFFI8664VYHD/@@download/IGVFFI8664VYHD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4ae46183-86f3-40f4-b35d-514bdddb6cae/IGVFFI8664VYHD.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-2213_L7_SS-PKR-533_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7160GJNZ/",
"accession": "IGVFFI7160GJNZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8303_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:11.144378+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI7160GJNZ/@@download/IGVFFI7160GJNZ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/9fae4d95-13c1-4a08-9c7e-61e81e18a4f5/IGVFFI7160GJNZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8303_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2199JMYY/",
"accession": "IGVFFI2199JMYY",
"aliases": [
"buenrostro-bernstein:SS-LS_8359_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:28.179368+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI2199JMYY/@@download/IGVFFI2199JMYY.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/5fe1511a-83c7-43c3-9eab-1ab835adc2c2/IGVFFI2199JMYY.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8359_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8871DRGI/"
],
"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/IGVFDS7911YQZW/",
"accession": "IGVFDS7911YQZW",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:59.800928+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1072XOVT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1072XOVT",
"aliases": [
"buenrostro-bernstein:BioSam 5151_SS-PKR 533"
],
"cellular_sub_pool": "SS-PKR 533",
"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 533)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:27.162665+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "c0a321c1-4da6-4d9a-b3db-363c6b0520df"
}