{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9866LFTQ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9866LFTQ",
"aliases": [
"buenrostro-bernstein:scRNA Lib 597"
],
"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 [IGVFSM2881UHTO](/tissues/IGVFSM2881UHTO/) 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/IGVFSM2881UHTO/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9866LFTQ](/measurement-sets/IGVFDS9866LFTQ/) 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/IGVFDS9866LFTQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9866LFTQ](/measurement-sets/IGVFDS9866LFTQ/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9866LFTQ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9866LFTQ](/measurement-sets/IGVFDS9866LFTQ/) has in progress subobject tabular file [IGVFFI9034HUWG](/tabular-files/IGVFFI9034HUWG/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9866LFTQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9866LFTQ](/measurement-sets/IGVFDS9866LFTQ/) 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/IGVFDS9866LFTQ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM2881UHTO](/tissues/IGVFSM2881UHTO/) 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/IGVFSM2881UHTO/"
}
]
},
"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": "2025-03-09T15:52:18.631545+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9446AKYF/",
"accession": "IGVFDO9446AKYF",
"aliases": [
"buenrostro-bernstein:Donor 2047"
],
"sex": "unspecified",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4949HHAZ/",
"accession": "IGVFFI4949HHAZ",
"aliases": [
"buenrostro-bernstein:SS-LS_3807_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:22.123960+00:00",
"file_format": "fastq",
"file_size": 919765448,
"href": "/sequence-files/IGVFFI4949HHAZ/@@download/IGVFFI4949HHAZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/7697cd80-188f-4b42-a4c7-6a8d208e3cac/IGVFFI4949HHAZ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1535_L1_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1199GCIN/",
"accession": "IGVFFI1199GCIN",
"aliases": [
"buenrostro-bernstein:SS-LS_3807_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:20.570926+00:00",
"file_format": "fastq",
"file_size": 562498725,
"href": "/sequence-files/IGVFFI1199GCIN/@@download/IGVFFI1199GCIN.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/48820f19-23eb-4e26-9206-9f22f2a56bd8/IGVFFI1199GCIN.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1535_L1_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0834RTNI/",
"accession": "IGVFFI0834RTNI",
"aliases": [
"buenrostro-bernstein:SS-LS_3831_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:02.875621+00:00",
"file_format": "fastq",
"file_size": 570251152,
"href": "/sequence-files/IGVFFI0834RTNI/@@download/IGVFFI0834RTNI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/a739671f-ff2e-4c11-8d1a-d9180e2cf491/IGVFFI0834RTNI.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1535_L2_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9814XYUH/",
"accession": "IGVFFI9814XYUH",
"aliases": [
"buenrostro-bernstein:SS-LS_3831_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-09T16:01:04.106111+00:00",
"file_format": "fastq",
"file_size": 938266654,
"href": "/sequence-files/IGVFFI9814XYUH/@@download/IGVFFI9814XYUH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/09/144d1ebc-c7c8-47dd-8a9f-36bb27fb668b/IGVFFI9814XYUH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-1535_L2_SS-PKR-434_2022-APRIL-R1-SET-OF-192_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2764HFQD/",
"accession": "IGVFFI2764HFQD",
"aliases": [
"buenrostro-bernstein:SS-LS_3831_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-13T17:54:29.411071+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI2764HFQD/@@download/IGVFFI2764HFQD.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/13/8fb8b7d1-c83a-4f51-9317-1e50b6eb3872/IGVFFI2764HFQD.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_3831_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2622TPEI/",
"accession": "IGVFFI2622TPEI",
"aliases": [
"buenrostro-bernstein:SS-LS_3807_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-13T17:54:38.784968+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI2622TPEI/@@download/IGVFFI2622TPEI.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/13/44d98b5c-fc9e-44c3-ab40-50fa30a1442b/IGVFFI2622TPEI.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/pilot-mouse-brain-new-pkr/SS-LS_3807_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2240UYEO/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 5,
"onlist_files": [
"/tabular-files/IGVFFI9034HUWG/",
"/tabular-files/IGVFFI0400MBIM/"
],
"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/IGVFDS7938OXSK/",
"accession": "IGVFDS7938OXSK",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4653HFNR/",
"accession": "IGVFDS4653HFNR",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS1816FCQL/",
"accession": "IGVFDS1816FCQL",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8623UWKX/",
"accession": "IGVFDS8623UWKX",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:24.619823+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM2881UHTO/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM2881UHTO",
"aliases": [
"buenrostro-bernstein:BioSam 4965_SS-PKR 434"
],
"cellular_sub_pool": "SS-PKR 434",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "brain",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 brain tissue (cellular sub pool: SS-PKR 434)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-09T16:01:02.875621+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "2fe83fdc-e376-4ed5-93b4-17569b877572"
}