{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5070VAJZ/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5070VAJZ",
"aliases": [
"buenrostro-bernstein:scRNA Lib 811"
],
"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": "Tissue [IGVFSM7633DIYU](/tissues/IGVFSM7633DIYU/) 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/IGVFSM7633DIYU/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS5070VAJZ](/measurement-sets/IGVFDS5070VAJZ/) 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/IGVFDS5070VAJZ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5070VAJZ](/measurement-sets/IGVFDS5070VAJZ/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5070VAJZ/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS5070VAJZ](/measurement-sets/IGVFDS5070VAJZ/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS5070VAJZ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5070VAJZ](/measurement-sets/IGVFDS5070VAJZ/) 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/IGVFDS5070VAJZ/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM7633DIYU](/tissues/IGVFSM7633DIYU/) 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/IGVFSM7633DIYU/"
}
]
},
"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": "2025-03-05T15:34:34.754852+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO7272VQKZ/",
"accession": "IGVFDO7272VQKZ",
"aliases": [
"ali-mortazavi:770_CASTJ_10F",
"buenrostro-bernstein:Donor 2072"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI2102JPNZ/",
"accession": "IGVFFI2102JPNZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8364_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:08.125104+00:00",
"file_format": "fastq",
"file_size": 2274644961,
"href": "/sequence-files/IGVFFI2102JPNZ/@@download/IGVFFI2102JPNZ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/428a0afd-8a44-43a2-9746-d646ea8e7f52/IGVFFI2102JPNZ.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-2218_L7_SS-PKR-576_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3519SGYS/",
"accession": "IGVFFI3519SGYS",
"aliases": [
"buenrostro-bernstein:SS-LS_8324_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:56.574734+00:00",
"file_format": "fastq",
"file_size": 2490357971,
"href": "/sequence-files/IGVFFI3519SGYS/@@download/IGVFFI3519SGYS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/426c7596-2d66-40c8-b0fa-26757dfb477f/IGVFFI3519SGYS.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-2178_L7_SS-PKR-576_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0000ICXC/",
"accession": "IGVFFI0000ICXC",
"aliases": [
"buenrostro-bernstein:SS-LS_8364_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:04.990886+00:00",
"file_format": "fastq",
"file_size": 1333142146,
"href": "/sequence-files/IGVFFI0000ICXC/@@download/IGVFFI0000ICXC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/52883f06-90d3-4f23-b84d-5e258042a1b7/IGVFFI0000ICXC.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-2218_L7_SS-PKR-576_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4266SEKD/",
"accession": "IGVFFI4266SEKD",
"aliases": [
"buenrostro-bernstein:SS-LS_8324_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:58.605803+00:00",
"file_format": "fastq",
"file_size": 4278930009,
"href": "/sequence-files/IGVFFI4266SEKD/@@download/IGVFFI4266SEKD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9aba9c49-8700-41b6-bf4a-f98686ac9382/IGVFFI4266SEKD.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-2178_L7_SS-PKR-576_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2186SFSP/",
"accession": "IGVFFI2186SFSP",
"aliases": [
"buenrostro-bernstein:SS-LS_8324_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:15.519001+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI2186SFSP/@@download/IGVFFI2186SFSP.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/3c0814e9-a398-47bd-a240-c24928925c3b/IGVFFI2186SFSP.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8324_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7429SDET/",
"accession": "IGVFFI7429SDET",
"aliases": [
"buenrostro-bernstein:SS-LS_8364_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:32.349189+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI7429SDET/@@download/IGVFFI7429SDET.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/cb02f091-847b-47f0-82c8-912f316573aa/IGVFFI7429SDET.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8364_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5871SKHT/"
],
"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/IGVFDS4624JCMI/",
"accession": "IGVFDS4624JCMI",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:48.925266+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM7633DIYU/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7633DIYU",
"aliases": [
"buenrostro-bernstein:BioSam 5149_SS-PKR 576"
],
"cellular_sub_pool": "SS-PKR 576",
"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 576)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:56.574734+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "d486e610-770c-4659-81f9-76c1eca7d2a0"
}