{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1530NDJN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1530NDJN",
"aliases": [
"buenrostro-bernstein:scRNA Lib 839"
],
"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 [IGVFSM9638OVAV](/tissues/IGVFSM9638OVAV/) 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/IGVFSM9638OVAV/"
},
{
"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 [IGVFDS1530NDJN](/measurement-sets/IGVFDS1530NDJN/) 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/IGVFDS1530NDJN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1530NDJN](/measurement-sets/IGVFDS1530NDJN/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1530NDJN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1530NDJN](/measurement-sets/IGVFDS1530NDJN/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1530NDJN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1530NDJN](/measurement-sets/IGVFDS1530NDJN/) 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/IGVFDS1530NDJN/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9638OVAV](/tissues/IGVFSM9638OVAV/) 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/IGVFSM9638OVAV/"
}
]
},
"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": "2025-03-05T15:34:45.170664+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO8443MWJY/",
"accession": "IGVFDO8443MWJY",
"aliases": [
"ali-mortazavi:773_CASTJ_10M",
"buenrostro-bernstein:Donor 2071"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI9924ARAF/",
"accession": "IGVFFI9924ARAF",
"aliases": [
"buenrostro-bernstein:SS-LS_8400_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:25.717998+00:00",
"file_format": "fastq",
"file_size": 4024411486,
"href": "/sequence-files/IGVFFI9924ARAF/@@download/IGVFFI9924ARAF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f3fb6e64-9115-4558-93e6-e8f2592247db/IGVFFI9924ARAF.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-2240_L1_SS-PKR-602_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1755BOTF/",
"accession": "IGVFFI1755BOTF",
"aliases": [
"buenrostro-bernstein:SS-LS_8410_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:49.149143+00:00",
"file_format": "fastq",
"file_size": 6893794067,
"href": "/sequence-files/IGVFFI1755BOTF/@@download/IGVFFI1755BOTF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f6f47593-ffd6-4ed2-a286-72c2c75edfc4/IGVFFI1755BOTF.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-2240_L2_SS-PKR-602_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6505CMQF/",
"accession": "IGVFFI6505CMQF",
"aliases": [
"buenrostro-bernstein:SS-LS_8420_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:11.425574+00:00",
"file_format": "fastq",
"file_size": 6879278340,
"href": "/sequence-files/IGVFFI6505CMQF/@@download/IGVFFI6505CMQF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/2a82c5c8-8e1b-40dc-98f1-6dc8ab6431cd/IGVFFI6505CMQF.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-2240_L3_SS-PKR-602_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0765XTWT/",
"accession": "IGVFFI0765XTWT",
"aliases": [
"buenrostro-bernstein:SS-LS_8400_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:28.040678+00:00",
"file_format": "fastq",
"file_size": 6917088595,
"href": "/sequence-files/IGVFFI0765XTWT/@@download/IGVFFI0765XTWT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f34d73ad-b1f7-4537-8acd-e48e41aa6a46/IGVFFI0765XTWT.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-2240_L1_SS-PKR-602_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4503CYVL/",
"accession": "IGVFFI4503CYVL",
"aliases": [
"buenrostro-bernstein:SS-LS_8420_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:08.667274+00:00",
"file_format": "fastq",
"file_size": 4004327170,
"href": "/sequence-files/IGVFFI4503CYVL/@@download/IGVFFI4503CYVL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5c94cbe7-380a-4570-aa64-2761a99bf663/IGVFFI4503CYVL.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-2240_L3_SS-PKR-602_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1267XNFK/",
"accession": "IGVFFI1267XNFK",
"aliases": [
"buenrostro-bernstein:SS-LS_8410_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:46.608875+00:00",
"file_format": "fastq",
"file_size": 4018919504,
"href": "/sequence-files/IGVFFI1267XNFK/@@download/IGVFFI1267XNFK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d98d4e49-57d8-41a8-807b-640c81193006/IGVFFI1267XNFK.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2240_L2_SS-PKR-602_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2491LVKG/",
"accession": "IGVFFI2491LVKG",
"aliases": [
"buenrostro-bernstein:SS-LS_8400_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:39.182966+00:00",
"file_format": "yaml",
"file_size": 1286,
"href": "/configuration-files/IGVFFI2491LVKG/@@download/IGVFFI2491LVKG.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/9fef331c-7dc8-443d-96fa-e6e7ffbf1898/IGVFFI2491LVKG.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8400_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3189ISOM/",
"accession": "IGVFFI3189ISOM",
"aliases": [
"buenrostro-bernstein:SS-LS_8410_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:49.144833+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI3189ISOM/@@download/IGVFFI3189ISOM.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/8df304cb-db90-4726-bfa3-581d9f5042de/IGVFFI3189ISOM.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8410_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4908NRNE/",
"accession": "IGVFFI4908NRNE",
"aliases": [
"buenrostro-bernstein:SS-LS_8420_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:59.746392+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI4908NRNE/@@download/IGVFFI4908NRNE.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/3d2bd9ce-7a5e-48f5-9994-b92c192bb216/IGVFFI4908NRNE.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8420_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS1883ZXNX/"
],
"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/IGVFDS0421VWRP/",
"accession": "IGVFDS0421VWRP",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:48.211779+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9638OVAV/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9638OVAV",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 602"
],
"cellular_sub_pool": "SS-PKR 602",
"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 (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 602)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T16:00:25.717998+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "ebae932b-6946-4296-a373-968274053a2f"
}