{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3683ZDLI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3683ZDLI",
"aliases": [
"buenrostro-bernstein:scRNA Lib 795"
],
"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 [IGVFSM5118GDEW](/tissues/IGVFSM5118GDEW/) 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/IGVFSM5118GDEW/"
},
{
"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 [IGVFDS3683ZDLI](/measurement-sets/IGVFDS3683ZDLI/) 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/IGVFDS3683ZDLI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3683ZDLI](/measurement-sets/IGVFDS3683ZDLI/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3683ZDLI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS3683ZDLI](/measurement-sets/IGVFDS3683ZDLI/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS3683ZDLI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3683ZDLI](/measurement-sets/IGVFDS3683ZDLI/) 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/IGVFDS3683ZDLI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM5118GDEW](/tissues/IGVFSM5118GDEW/) 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/IGVFSM5118GDEW/"
}
]
},
"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": "2025-03-05T15:34:16.949624+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO9355TCPX/",
"accession": "IGVFDO9355TCPX",
"aliases": [
"ali-mortazavi:777_CASTJ_10M",
"buenrostro-bernstein:Donor 2073"
],
"sex": "male",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI5024XRPO/",
"accession": "IGVFFI5024XRPO",
"aliases": [
"buenrostro-bernstein:SS-LS_7397_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:45.509543+00:00",
"file_format": "fastq",
"file_size": 16492002750,
"href": "/sequence-files/IGVFFI5024XRPO/@@download/IGVFFI5024XRPO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5b3274d8-7692-4303-951a-cb7b3acaf169/IGVFFI5024XRPO.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-1956_L7_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7275NLIB/",
"accession": "IGVFFI7275NLIB",
"aliases": [
"buenrostro-bernstein:SS-LS_7403_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:55.242889+00:00",
"file_format": "fastq",
"file_size": 9075576261,
"href": "/sequence-files/IGVFFI7275NLIB/@@download/IGVFFI7275NLIB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/e340d129-2e3e-48b5-9b3e-b8f7789ab127/IGVFFI7275NLIB.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-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5329BVER/",
"accession": "IGVFFI5329BVER",
"aliases": [
"buenrostro-bernstein:SS-LS_7397_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:42.624367+00:00",
"file_format": "fastq",
"file_size": 9272497544,
"href": "/sequence-files/IGVFFI5329BVER/@@download/IGVFFI5329BVER.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/c5c4ba08-8d57-4668-bb6b-73e73bc48316/IGVFFI5329BVER.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-1956_L7_SS-PKR-500_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8599LHBE/",
"accession": "IGVFFI8599LHBE",
"aliases": [
"buenrostro-bernstein:SS-LS_7403_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:57.102143+00:00",
"file_format": "fastq",
"file_size": 15868581523,
"href": "/sequence-files/IGVFFI8599LHBE/@@download/IGVFFI8599LHBE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/849e64ae-ca71-4fb6-8863-6b5442208d78/IGVFFI8599LHBE.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-1956_L8_SS-PKR-500_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1292VUYI/",
"accession": "IGVFFI1292VUYI",
"aliases": [
"buenrostro-bernstein:SS-LS_7397_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:57:57.359757+00:00",
"file_format": "yaml",
"file_size": 1293,
"href": "/configuration-files/IGVFFI1292VUYI/@@download/IGVFFI1292VUYI.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/fcbcfac5-feed-4e19-9308-d669185fd659/IGVFFI1292VUYI.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7397_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9464LOTZ/",
"accession": "IGVFFI9464LOTZ",
"aliases": [
"buenrostro-bernstein:SS-LS_7403_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:03.495665+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI9464LOTZ/@@download/IGVFFI9464LOTZ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/44b5dcc8-003d-43fe-8afa-91d4b30b0171/IGVFFI9464LOTZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7403_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5790TJZR/"
],
"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/IGVFDS8255ZBNK/",
"accession": "IGVFDS8255ZBNK",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:09.536846+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM5118GDEW/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5118GDEW",
"aliases": [
"buenrostro-bernstein:BioSam 5150_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 CASTJ (male) 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": "2025-03-05T15:56:42.624367+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "d35409e9-96a7-4661-a323-e8c3f4ae3bf5"
}