{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0026GUHT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0026GUHT",
"aliases": [
"buenrostro-bernstein:scRNA Lib 802"
],
"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 [IGVFDS0026GUHT](/measurement-sets/IGVFDS0026GUHT/) 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/IGVFDS0026GUHT/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0026GUHT](/measurement-sets/IGVFDS0026GUHT/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0026GUHT/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0026GUHT](/measurement-sets/IGVFDS0026GUHT/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0026GUHT/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM8703CYDR](/tissues/IGVFSM8703CYDR/) 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/IGVFSM8703CYDR/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0026GUHT](/measurement-sets/IGVFDS0026GUHT/) 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/IGVFDS0026GUHT/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM8703CYDR](/tissues/IGVFSM8703CYDR/) 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/IGVFSM8703CYDR/"
}
]
},
"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": "2025-03-05T15:34:23.508855+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/IGVFFI6139NSPC/",
"accession": "IGVFFI6139NSPC",
"aliases": [
"buenrostro-bernstein:SS-LS_8355_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:48.417667+00:00",
"file_format": "fastq",
"file_size": 3156638923,
"href": "/sequence-files/IGVFFI6139NSPC/@@download/IGVFFI6139NSPC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/0c679a62-792e-4989-84c6-c056cadaca5c/IGVFFI6139NSPC.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-2209_L7_SS-PKR-530_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1622TFLF/",
"accession": "IGVFFI1622TFLF",
"aliases": [
"buenrostro-bernstein:SS-LS_8299_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:19.463009+00:00",
"file_format": "fastq",
"file_size": 6411586786,
"href": "/sequence-files/IGVFFI1622TFLF/@@download/IGVFFI1622TFLF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/62424491-eb1e-46e1-9efb-2b77336bd976/IGVFFI1622TFLF.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-2169_L6_SS-PKR-530_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6472XNYJ/",
"accession": "IGVFFI6472XNYJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8355_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:50.226998+00:00",
"file_format": "fastq",
"file_size": 5420747322,
"href": "/sequence-files/IGVFFI6472XNYJ/@@download/IGVFFI6472XNYJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/53188e37-5ec4-4188-8c9c-507bb686405c/IGVFFI6472XNYJ.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-2209_L7_SS-PKR-530_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6787OION/",
"accession": "IGVFFI6787OION",
"aliases": [
"buenrostro-bernstein:SS-LS_8299_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:21.463474+00:00",
"file_format": "fastq",
"file_size": 11855845961,
"href": "/sequence-files/IGVFFI6787OION/@@download/IGVFFI6787OION.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/69bfd54f-07c2-42d9-8a39-e094a6814b21/IGVFFI6787OION.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-2169_L6_SS-PKR-530_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7593XCYG/",
"accession": "IGVFFI7593XCYG",
"aliases": [
"buenrostro-bernstein:SS-LS_8355_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:24.299733+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI7593XCYG/@@download/IGVFFI7593XCYG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/292c2aa6-5fe7-49f3-9b4f-5fcb9b01169b/IGVFFI7593XCYG.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8355_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2882QTUP/",
"accession": "IGVFFI2882QTUP",
"aliases": [
"buenrostro-bernstein:SS-LS_8299_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:07.005081+00:00",
"file_format": "yaml",
"file_size": 1284,
"href": "/configuration-files/IGVFFI2882QTUP/@@download/IGVFFI2882QTUP.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/8f18ed92-f62c-4a06-af33-14309f9c8c64/IGVFFI2882QTUP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8299_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8692XJDQ/"
],
"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/IGVFDS1304DPTZ/",
"accession": "IGVFDS1304DPTZ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:46.540827+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM8703CYDR/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM8703CYDR",
"aliases": [
"buenrostro-bernstein:BioSam 5151_SS-PKR 530"
],
"cellular_sub_pool": "SS-PKR 530",
"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 530)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:19.463009+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "19639e4e-0b87-46d3-a9db-981caebb5dd7"
}