{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4731ODMK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4731ODMK",
"aliases": [
"buenrostro-bernstein:scRNA Lib 794"
],
"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 [IGVFSM6189KRRN](/tissues/IGVFSM6189KRRN/) 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/IGVFSM6189KRRN/"
},
{
"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 [IGVFDS4731ODMK](/measurement-sets/IGVFDS4731ODMK/) 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/IGVFDS4731ODMK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4731ODMK](/measurement-sets/IGVFDS4731ODMK/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4731ODMK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4731ODMK](/measurement-sets/IGVFDS4731ODMK/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4731ODMK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4731ODMK](/measurement-sets/IGVFDS4731ODMK/) 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/IGVFDS4731ODMK/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6189KRRN](/tissues/IGVFSM6189KRRN/) 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/IGVFSM6189KRRN/"
}
]
},
"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": "2025-03-05T15:33:39.691894+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO7484YDXT/",
"accession": "IGVFDO7484YDXT",
"aliases": [
"ali-mortazavi:766_B6J_10F",
"buenrostro-bernstein:Donor 2076"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI0418IGTG/",
"accession": "IGVFFI0418IGTG",
"aliases": [
"buenrostro-bernstein:SS-LS_7402_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:11.383652+00:00",
"file_format": "fastq",
"file_size": 11923282562,
"href": "/sequence-files/IGVFFI0418IGTG/@@download/IGVFFI0418IGTG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6eca1c4d-8007-4488-97e3-ca82b1b8741b/IGVFFI0418IGTG.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-1955_L8_SS-PKR-500_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5972BFUR/",
"accession": "IGVFFI5972BFUR",
"aliases": [
"buenrostro-bernstein:SS-LS_7396_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:57.476284+00:00",
"file_format": "fastq",
"file_size": 7070594298,
"href": "/sequence-files/IGVFFI5972BFUR/@@download/IGVFFI5972BFUR.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b56a45b4-70e0-4dd8-9e32-00511c723410/IGVFFI5972BFUR.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-1955_L7_SS-PKR-500_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5484CCRJ/",
"accession": "IGVFFI5484CCRJ",
"aliases": [
"buenrostro-bernstein:SS-LS_7396_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:59.585796+00:00",
"file_format": "fastq",
"file_size": 12417377462,
"href": "/sequence-files/IGVFFI5484CCRJ/@@download/IGVFFI5484CCRJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/262c07c4-a3d0-47f4-b4d0-275fcafffb77/IGVFFI5484CCRJ.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-1955_L7_SS-PKR-500_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3225JJJX/",
"accession": "IGVFFI3225JJJX",
"aliases": [
"buenrostro-bernstein:SS-LS_7402_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:52:09.726527+00:00",
"file_format": "fastq",
"file_size": 6908786579,
"href": "/sequence-files/IGVFFI3225JJJX/@@download/IGVFFI3225JJJX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/8ec7d164-a4c2-4b7a-9f5c-6ff05f741cc8/IGVFFI3225JJJX.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-1955_L8_SS-PKR-500_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9692UAPS/",
"accession": "IGVFFI9692UAPS",
"aliases": [
"buenrostro-bernstein:SS-LS_7402_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:56:43.261436+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI9692UAPS/@@download/IGVFFI9692UAPS.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/ca44723b-6919-4ef4-8ae2-4e3d5e956237/IGVFFI9692UAPS.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7402_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8921OVDO/",
"accession": "IGVFFI8921OVDO",
"aliases": [
"buenrostro-bernstein:SS-LS_7396_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:56:35.995837+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI8921OVDO/@@download/IGVFFI8921OVDO.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/38aec235-5410-4f93-9073-30b22a99bb40/IGVFFI8921OVDO.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7396_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8609VYFV/"
],
"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/IGVFDS9519NBWN/",
"accession": "IGVFDS9519NBWN",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:54.872615+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6189KRRN/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6189KRRN",
"aliases": [
"buenrostro-bernstein:BioSam 5153_SS-PKR 500"
],
"cellular_sub_pool": "SS-PKR 500",
"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 (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 500)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:51:57.476284+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "1848dece-9adc-4362-b1dc-d35ccd929091"
}