{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0618QCGG/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0618QCGG",
"aliases": [
"buenrostro-bernstein:scRNA Lib 800"
],
"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": "Measurement set [IGVFDS0618QCGG](/measurement-sets/IGVFDS0618QCGG/) 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/IGVFDS0618QCGG/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0618QCGG](/measurement-sets/IGVFDS0618QCGG/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0618QCGG/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0618QCGG](/measurement-sets/IGVFDS0618QCGG/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0618QCGG/"
},
{
"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 [IGVFSM6095NJDT](/tissues/IGVFSM6095NJDT/) 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/IGVFSM6095NJDT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0618QCGG](/measurement-sets/IGVFDS0618QCGG/) 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/IGVFDS0618QCGG/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6095NJDT](/tissues/IGVFSM6095NJDT/) 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/IGVFSM6095NJDT/"
}
]
},
"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": "2025-03-05T15:34:22.660128+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/IGVFFI6809GYBY/",
"accession": "IGVFFI6809GYBY",
"aliases": [
"buenrostro-bernstein:SS-LS_8353_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:44.922973+00:00",
"file_format": "fastq",
"file_size": 1834647804,
"href": "/sequence-files/IGVFFI6809GYBY/@@download/IGVFFI6809GYBY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/3cfd6104-0dc1-4c58-8527-df9a9fcd59da/IGVFFI6809GYBY.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-2207_L7_SS-PKR-528_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9566JQFA/",
"accession": "IGVFFI9566JQFA",
"aliases": [
"buenrostro-bernstein:SS-LS_8353_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:46.708748+00:00",
"file_format": "fastq",
"file_size": 2615390363,
"href": "/sequence-files/IGVFFI9566JQFA/@@download/IGVFFI9566JQFA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/9bc34922-2917-4fc8-af6b-71bb8c17aafa/IGVFFI9566JQFA.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-2207_L7_SS-PKR-528_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8739VSKK/",
"accession": "IGVFFI8739VSKK",
"aliases": [
"buenrostro-bernstein:SS-LS_8297_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:15.520543+00:00",
"file_format": "fastq",
"file_size": 4589594761,
"href": "/sequence-files/IGVFFI8739VSKK/@@download/IGVFFI8739VSKK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6cb605f6-b44b-4d68-9668-edbb9f63993d/IGVFFI8739VSKK.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-2167_L6_SS-PKR-528_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9109NWCS/",
"accession": "IGVFFI9109NWCS",
"aliases": [
"buenrostro-bernstein:SS-LS_8297_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:17.505699+00:00",
"file_format": "fastq",
"file_size": 7429053293,
"href": "/sequence-files/IGVFFI9109NWCS/@@download/IGVFFI9109NWCS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/e0fbccb4-20c8-4130-87f4-6c73b711a12a/IGVFFI9109NWCS.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-2167_L6_SS-PKR-528_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3732TKOK/",
"accession": "IGVFFI3732TKOK",
"aliases": [
"buenrostro-bernstein:SS-LS_8353_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:22.138161+00:00",
"file_format": "yaml",
"file_size": 1289,
"href": "/configuration-files/IGVFFI3732TKOK/@@download/IGVFFI3732TKOK.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/cf1c9e73-e0e0-4e7d-b9c6-6a35d66ac697/IGVFFI3732TKOK.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8353_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6154ISKO/",
"accession": "IGVFFI6154ISKO",
"aliases": [
"buenrostro-bernstein:SS-LS_8297_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:05.294952+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI6154ISKO/@@download/IGVFFI6154ISKO.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/7891905c-eb97-478a-8f20-8715ac77bb05/IGVFFI6154ISKO.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8297_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5668LOCH/"
],
"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/IGVFDS9742DJVE/",
"accession": "IGVFDS9742DJVE",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:45.549997+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6095NJDT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6095NJDT",
"aliases": [
"buenrostro-bernstein:BioSam 5151_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 CAST/EiJ (female) 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": "2025-03-05T15:57:15.520543+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "67c4d6db-2800-4030-a31b-2046c816ab64"
}