{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9947GKSM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9947GKSM",
"aliases": [
"buenrostro-bernstein:scRNA Lib 812"
],
"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 [IGVFDS9947GKSM](/measurement-sets/IGVFDS9947GKSM/) 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/IGVFDS9947GKSM/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9947GKSM](/measurement-sets/IGVFDS9947GKSM/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9947GKSM/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9947GKSM](/measurement-sets/IGVFDS9947GKSM/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9947GKSM/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM8298OVYF](/tissues/IGVFSM8298OVYF/) 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/IGVFSM8298OVYF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9947GKSM](/measurement-sets/IGVFDS9947GKSM/) 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/IGVFDS9947GKSM/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8298OVYF](/tissues/IGVFSM8298OVYF/) 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/IGVFSM8298OVYF/"
}
]
},
"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": "2025-03-05T17:52:41.775934+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"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/IGVFFI5982QYIU/",
"accession": "IGVFFI5982QYIU",
"aliases": [
"buenrostro-bernstein:SS-LS_8325_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:43.983149+00:00",
"file_format": "fastq",
"file_size": 14199966698,
"href": "/sequence-files/IGVFFI5982QYIU/@@download/IGVFFI5982QYIU.fastq.gz",
"md5sum": "1e5006064471d0741bebdc38fefda079",
"s3_uri": "s3://igvf-files/2025/03/05/18969eb3-1442-4a6b-af9d-732b9f7a7e93/IGVFFI5982QYIU.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-2179_L7_SS-PKR-583_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8590ABPQ/",
"accession": "IGVFFI8590ABPQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8325_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:41.841746+00:00",
"file_format": "fastq",
"file_size": 8187272964,
"href": "/sequence-files/IGVFFI8590ABPQ/@@download/IGVFFI8590ABPQ.fastq.gz",
"md5sum": "ace39bf3362bcac89e9c8e98dcdf244e",
"s3_uri": "s3://igvf-files/2025/03/05/69183d8b-7303-46fa-80bc-ad0b0ff94112/IGVFFI8590ABPQ.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-2179_L7_SS-PKR-583_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3885GAEG/",
"accession": "IGVFFI3885GAEG",
"aliases": [
"buenrostro-bernstein:SS-LS_8365_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:12.893164+00:00",
"file_format": "fastq",
"file_size": 7933859589,
"href": "/sequence-files/IGVFFI3885GAEG/@@download/IGVFFI3885GAEG.fastq.gz",
"md5sum": "a96620ca215abb2027009da71bb1d91e",
"s3_uri": "s3://igvf-files/2025/03/05/b3436871-1768-44be-a968-f11c0289a084/IGVFFI3885GAEG.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-2219_L7_SS-PKR-583_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8688AZMU/",
"accession": "IGVFFI8688AZMU",
"aliases": [
"buenrostro-bernstein:SS-LS_8365_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:11.396314+00:00",
"file_format": "fastq",
"file_size": 4621838715,
"href": "/sequence-files/IGVFFI8688AZMU/@@download/IGVFFI8688AZMU.fastq.gz",
"md5sum": "19f7f3b1ec72867d3f8a88d8036c5577",
"s3_uri": "s3://igvf-files/2025/03/05/b202c57e-b23f-4d7f-bd19-18125c036e01/IGVFFI8688AZMU.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-2219_L7_SS-PKR-583_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8340UCTH/",
"accession": "IGVFFI8340UCTH",
"aliases": [
"buenrostro-bernstein:SS-LS_8365_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:17.139321+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI8340UCTH/@@download/IGVFFI8340UCTH.yaml.gz",
"md5sum": "10e5f155ed6f1d161ea2a113e6974a4a",
"s3_uri": "s3://igvf-files/2025/03/07/58aa1dba-01df-4a11-bddf-dd87464852ce/IGVFFI8340UCTH.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8365_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3404SXLZ/",
"accession": "IGVFFI3404SXLZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8325_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:00.773520+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI3404SXLZ/@@download/IGVFFI3404SXLZ.yaml.gz",
"md5sum": "59dc1e00a08ed8487789161ba09169a1",
"s3_uri": "s3://igvf-files/2025/03/07/27c9ca79-aa96-46df-8189-2186687df4c3/IGVFFI3404SXLZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8325_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8078YEFX/"
],
"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/IGVFDS8130TGNJ/",
"accession": "IGVFDS8130TGNJ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:17.096839+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8298OVYF/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8298OVYF",
"aliases": [
"buenrostro-bernstein:BioSam 5154_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 C57BL/6J (male) 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": "2025-03-05T17:57:41.841746+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "ae9d34ae-7a2d-437a-8712-2e6b515786db"
}