{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS1149ZGJI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS1149ZGJI",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1781"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"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/"
},
{
"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 [IGVFDS1149ZGJI](/measurement-sets/IGVFDS1149ZGJI/) 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/IGVFDS1149ZGJI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1149ZGJI](/measurement-sets/IGVFDS1149ZGJI/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1149ZGJI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS1149ZGJI](/measurement-sets/IGVFDS1149ZGJI/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS1149ZGJI/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS1149ZGJI](/measurement-sets/IGVFDS1149ZGJI/) 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/IGVFDS1149ZGJI/"
}
],
"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": "2025-03-05T15:34:43.088579+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/IGVFFI4883FQAY/",
"accession": "IGVFFI4883FQAY",
"aliases": [
"buenrostro-bernstein:SS-LS_8386_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:53.937154+00:00",
"file_format": "fastq",
"file_size": 2806800274,
"href": "/sequence-files/IGVFFI4883FQAY/@@download/IGVFFI4883FQAY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/444c3b04-293d-4590-b357-da78d66de31b/IGVFFI4883FQAY.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-2256_L5_SS-PKR-605_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8443EAOL/",
"accession": "IGVFFI8443EAOL",
"aliases": [
"buenrostro-bernstein:SS-LS_8396_R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:15.712662+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI8443EAOL/@@download/IGVFFI8443EAOL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f158ac1a-3466-409f-a0dd-02ddb58e954c/IGVFFI8443EAOL.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-2256_L6_SS-PKR-605_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4184QDHJ/",
"accession": "IGVFFI4184QDHJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8376_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:33.192264+00:00",
"file_format": "fastq",
"file_size": 2802771435,
"href": "/sequence-files/IGVFFI4184QDHJ/@@download/IGVFFI4184QDHJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4e8caacf-d80a-44b7-8e77-2779b939950c/IGVFFI4184QDHJ.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-2256_L4_SS-PKR-605_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9668YPPC/",
"accession": "IGVFFI9668YPPC",
"aliases": [
"buenrostro-bernstein:SS-LS_8396_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T16:00:18.925144+00:00",
"file_format": "fastq",
"file_size": 3881557846,
"href": "/sequence-files/IGVFFI9668YPPC/@@download/IGVFFI9668YPPC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/54b185cc-c07a-4606-ad6c-bc882dcc703d/IGVFFI9668YPPC.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-2256_L6_SS-PKR-605_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6598DNMV/",
"accession": "IGVFFI6598DNMV",
"aliases": [
"buenrostro-bernstein:SS-LS_8386_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:56.518839+00:00",
"file_format": "fastq",
"file_size": 3877147157,
"href": "/sequence-files/IGVFFI6598DNMV/@@download/IGVFFI6598DNMV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/cda0c127-720c-4114-b3e5-b1bc734c957d/IGVFFI6598DNMV.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-2256_L5_SS-PKR-605_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2344WJQL/",
"accession": "IGVFFI2344WJQL",
"aliases": [
"buenrostro-bernstein:SS-LS_8376_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:59:35.071392+00:00",
"file_format": "fastq",
"file_size": 3894062868,
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"s3_uri": "s3://igvf-files/2025/03/05/e9bbe49c-c785-4a4f-a387-9a9c6b522d29/IGVFFI2344WJQL.fastq.gz",
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
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"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2256_L4_SS-PKR-605_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI1508FDIS/",
"accession": "IGVFFI1508FDIS",
"aliases": [
"buenrostro-bernstein:SS-LS_8386_seqspec"
],
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"creation_timestamp": "2025-03-07T20:01:30.809950+00:00",
"file_format": "yaml",
"file_size": 1252,
"href": "/configuration-files/IGVFFI1508FDIS/@@download/IGVFFI1508FDIS.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/2a5f6e5a-074b-432d-80bb-a9aec2acd6ed/IGVFFI1508FDIS.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8386_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5933EMEO/",
"accession": "IGVFFI5933EMEO",
"aliases": [
"buenrostro-bernstein:SS-LS_8396_seqspec"
],
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"creation_timestamp": "2025-03-07T20:01:41.373712+00:00",
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"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5698PWWS/",
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"buenrostro-bernstein:SS-LS_8376_seqspec"
],
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8376_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": [
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"/tabular-files/IGVFFI2668ZFEB/"
],
"onlist_method": "product",
"preferred_assay_title": "SHARE-seq",
"protocols": [
"https://www.protocols.io/view/share-seq-protocol-v2-2-di3y4gpw"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS1483XTRT/",
"accession": "IGVFDS1483XTRT",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:50.360403+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": {
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"title": "Siddarth Wekhande"
},
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"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "8f3620cf-88ce-486e-90c7-60db0720ff9f"
}