{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3193DFSP/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3193DFSP",
"aliases": [
"buenrostro-bernstein:scRNA Lib 801"
],
"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 [IGVFSM8139LSOK](/tissues/IGVFSM8139LSOK/) 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/IGVFSM8139LSOK/"
},
{
"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 [IGVFDS3193DFSP](/measurement-sets/IGVFDS3193DFSP/) 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/IGVFDS3193DFSP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3193DFSP](/measurement-sets/IGVFDS3193DFSP/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3193DFSP/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3193DFSP](/measurement-sets/IGVFDS3193DFSP/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3193DFSP/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3193DFSP](/measurement-sets/IGVFDS3193DFSP/) 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/IGVFDS3193DFSP/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8139LSOK](/tissues/IGVFSM8139LSOK/) 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/IGVFSM8139LSOK/"
}
]
},
"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": "2025-03-05T15:33:45.691737+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO0972REDW/",
"accession": "IGVFDO0972REDW",
"aliases": [
"ali-mortazavi:767_B6J_10M",
"buenrostro-bernstein:Donor 2075"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7907IMZV/",
"accession": "IGVFFI7907IMZV",
"aliases": [
"buenrostro-bernstein:SS-LS_8354_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:40.199674+00:00",
"file_format": "fastq",
"file_size": 3197371802,
"href": "/sequence-files/IGVFFI7907IMZV/@@download/IGVFFI7907IMZV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/be6d0885-1519-4204-9fc2-b9b6e2a15940/IGVFFI7907IMZV.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-2208_L7_SS-PKR-528_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3881YGKA/",
"accession": "IGVFFI3881YGKA",
"aliases": [
"buenrostro-bernstein:SS-LS_8298_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:32.457296+00:00",
"file_format": "fastq",
"file_size": 5758240551,
"href": "/sequence-files/IGVFFI3881YGKA/@@download/IGVFFI3881YGKA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/dcec9451-3e5a-4890-9392-c994ecee1a5c/IGVFFI3881YGKA.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-2168_L6_SS-PKR-528_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7790OWFM/",
"accession": "IGVFFI7790OWFM",
"aliases": [
"buenrostro-bernstein:SS-LS_8298_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:34.401254+00:00",
"file_format": "fastq",
"file_size": 9296904488,
"href": "/sequence-files/IGVFFI7790OWFM/@@download/IGVFFI7790OWFM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5fab5602-510f-481b-b4c8-652f13b19d3f/IGVFFI7790OWFM.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-2168_L6_SS-PKR-528_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3980RFHW/",
"accession": "IGVFFI3980RFHW",
"aliases": [
"buenrostro-bernstein:SS-LS_8354_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:53:37.698476+00:00",
"file_format": "fastq",
"file_size": 2250950695,
"href": "/sequence-files/IGVFFI3980RFHW/@@download/IGVFFI3980RFHW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/296367ab-c711-4631-aba3-cb267ad2faf0/IGVFFI3980RFHW.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-2208_L7_SS-PKR-528_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6708DIXF/",
"accession": "IGVFFI6708DIXF",
"aliases": [
"buenrostro-bernstein:SS-LS_8354_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:04.719037+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI6708DIXF/@@download/IGVFFI6708DIXF.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/0bce8773-6b15-4eb2-a008-b5c68ba8d8c1/IGVFFI6708DIXF.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8354_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6090EETF/",
"accession": "IGVFFI6090EETF",
"aliases": [
"buenrostro-bernstein:SS-LS_8298_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:56:47.660965+00:00",
"file_format": "yaml",
"file_size": 1285,
"href": "/configuration-files/IGVFFI6090EETF/@@download/IGVFFI6090EETF.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/f43ee606-fc40-4dd2-a9fc-0cb1ccbf0df7/IGVFFI6090EETF.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8298_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS9783INQU/"
],
"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/IGVFDS4094SFYZ/",
"accession": "IGVFDS4094SFYZ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:49.633389+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8139LSOK/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8139LSOK",
"aliases": [
"buenrostro-bernstein:BioSam 5152_SS-PKR 528"
],
"cellular_sub_pool": "SS-PKR 528",
"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 528)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:52:32.457296+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "4e04cc0b-82e4-463d-b244-8a9f61125609"
}