{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1483XTRT/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1483XTRT",
"aliases": [
"buenrostro-bernstein:scRNA Lib 845"
],
"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": "Measurement set [IGVFDS1483XTRT](/measurement-sets/IGVFDS1483XTRT/) 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/IGVFDS1483XTRT/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1483XTRT](/measurement-sets/IGVFDS1483XTRT/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1483XTRT/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1483XTRT](/measurement-sets/IGVFDS1483XTRT/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1483XTRT/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM5413AOMQ](/tissues/IGVFSM5413AOMQ/) 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/IGVFSM5413AOMQ/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1483XTRT](/measurement-sets/IGVFDS1483XTRT/) 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/IGVFDS1483XTRT/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM5413AOMQ](/tissues/IGVFSM5413AOMQ/) 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/IGVFSM5413AOMQ/"
}
]
},
"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": "2025-03-05T15:34:48.373956+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/IGVFFI2328MBIG/",
"accession": "IGVFFI2328MBIG",
"aliases": [
"buenrostro-bernstein:SS-LS_8406_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:40.669452+00:00",
"file_format": "fastq",
"file_size": 5870339230,
"href": "/sequence-files/IGVFFI2328MBIG/@@download/IGVFFI2328MBIG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/32d7baed-9947-4005-ace9-9406908dfd76/IGVFFI2328MBIG.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-2246_L1_SS-PKR-605_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9308BFOT/",
"accession": "IGVFFI9308BFOT",
"aliases": [
"buenrostro-bernstein:SS-LS_8416_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:59.692765+00:00",
"file_format": "fastq",
"file_size": 3407680563,
"href": "/sequence-files/IGVFFI9308BFOT/@@download/IGVFFI9308BFOT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/99dfad41-a570-4d26-b610-99167e33e696/IGVFFI9308BFOT.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-2246_L2_SS-PKR-605_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9673GHTM/",
"accession": "IGVFFI9673GHTM",
"aliases": [
"buenrostro-bernstein:SS-LS_8406_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:38.851451+00:00",
"file_format": "fastq",
"file_size": 3419247327,
"href": "/sequence-files/IGVFFI9673GHTM/@@download/IGVFFI9673GHTM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b0665725-60b8-4138-b92e-687ea742ddc9/IGVFFI9673GHTM.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-2246_L1_SS-PKR-605_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3798QKXT/",
"accession": "IGVFFI3798QKXT",
"aliases": [
"buenrostro-bernstein:SS-LS_8426_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:23.914642+00:00",
"file_format": "fastq",
"file_size": 5846252869,
"href": "/sequence-files/IGVFFI3798QKXT/@@download/IGVFFI3798QKXT.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a23ba404-85c5-43f5-ab31-e4965f0c8964/IGVFFI3798QKXT.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-2246_L3_SS-PKR-605_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0558HFQX/",
"accession": "IGVFFI0558HFQX",
"aliases": [
"buenrostro-bernstein:SS-LS_8416_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:01.942353+00:00",
"file_format": "fastq",
"file_size": 5835379036,
"href": "/sequence-files/IGVFFI0558HFQX/@@download/IGVFFI0558HFQX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/331269d6-458e-4ff3-857a-15b420ec6f98/IGVFFI0558HFQX.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-2246_L2_SS-PKR-605_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8996KALC/",
"accession": "IGVFFI8996KALC",
"aliases": [
"buenrostro-bernstein:SS-LS_8426_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:01:22.057153+00:00",
"file_format": "fastq",
"file_size": 3407992900,
"href": "/sequence-files/IGVFFI8996KALC/@@download/IGVFFI8996KALC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/e6975c37-4e8a-470e-85ea-ad1e63be4b55/IGVFFI8996KALC.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-2246_L3_SS-PKR-605_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0720BYLL/",
"accession": "IGVFFI0720BYLL",
"aliases": [
"buenrostro-bernstein:SS-LS_8406_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:58:45.164966+00:00",
"file_format": "yaml",
"file_size": 1287,
"href": "/configuration-files/IGVFFI0720BYLL/@@download/IGVFFI0720BYLL.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/02b9acc8-9199-4214-8082-3392523dc2b2/IGVFFI0720BYLL.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8406_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4367JVHW/",
"accession": "IGVFFI4367JVHW",
"aliases": [
"buenrostro-bernstein:SS-LS_8416_seqspec"
],
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"creation_timestamp": "2025-03-07T19:58:55.918830+00:00",
"file_format": "yaml",
"file_size": 1288,
"href": "/configuration-files/IGVFFI4367JVHW/@@download/IGVFFI4367JVHW.yaml.gz",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8416_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0104GCTI/",
"accession": "IGVFFI0104GCTI",
"aliases": [
"buenrostro-bernstein:SS-LS_8426_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:07.387636+00:00",
"file_format": "yaml",
"file_size": 1283,
"href": "/configuration-files/IGVFFI0104GCTI/@@download/IGVFFI0104GCTI.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/83f7417f-0ea8-42c5-b058-75cbacfebb20/IGVFFI0104GCTI.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8426_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS5939RDPM/"
],
"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/IGVFDS1149ZGJI/",
"accession": "IGVFDS1149ZGJI",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:04.429180+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM5413AOMQ/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5413AOMQ",
"aliases": [
"buenrostro-bernstein:BioSam 5148_SS-PKR 605"
],
"cellular_sub_pool": "SS-PKR 605",
"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 605)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T16:00:38.851451+00:00",
"summary": "single-cell RNA sequencing assay (SHARE-seq)",
"uuid": "acaea3e4-eae5-408b-bc88-0a0b2837c12a"
}