{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0020LQRY/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0020LQRY",
"aliases": [
"bradley-bernstein:scATAC Lib 111",
"buenrostro-bernstein:scATAC Lib 111"
],
"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": "Measurement set [IGVFDS0020LQRY](/measurement-sets/IGVFDS0020LQRY/) 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/IGVFDS0020LQRY/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0020LQRY](/measurement-sets/IGVFDS0020LQRY/) has in progress subobject tabular file [IGVFFI0400MBIM](/tabular-files/IGVFFI0400MBIM/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0020LQRY/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0020LQRY](/measurement-sets/IGVFDS0020LQRY/) 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/IGVFDS0020LQRY/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM3932SXVT](/tissues/IGVFSM3932SXVT/) 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/IGVFSM3932SXVT/"
}
]
},
"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": "2023-08-28T20:29:05.273115+00:00",
"data_use_limitation_summaries": [
"no certificate"
],
"donors": [
{
"@id": "/rodent-donors/IGVFDO1318PLKS/",
"accession": "IGVFDO1318PLKS",
"aliases": [
"bradley-bernstein:Donor 1503",
"buenrostro-bernstein:Donor 1503"
],
"sex": "female",
"status": "released",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1847DJVR/",
"accession": "IGVFFI1847DJVR",
"aliases": [
"bradley-bernstein:SS-LS_2003_R1",
"bradley-bernstein:SS-LS_41_R1",
"buenrostro-bernstein:SS-LS_2003_R1",
"buenrostro-bernstein:SS-LS_41_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-01T20:25:55.381680+00:00",
"file_format": "fastq",
"file_size": 640679775,
"href": "/sequence-files/IGVFFI1847DJVR/@@download/IGVFFI1847DJVR.fastq.gz",
"md5sum": "d1e993df612ce2b1b87411336a3432f4",
"s3_uri": "s3://igvf-files/2023/09/01/992203a8-eb3f-4123-81a5-ce5b0a3d0c62/IGVFFI1847DJVR.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-156_L1_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0003RJLQ/",
"accession": "IGVFFI0003RJLQ",
"aliases": [
"bradley-bernstein:SS-LS_2003_R2",
"bradley-bernstein:SS-LS_41_R2",
"buenrostro-bernstein:SS-LS_2003_R2",
"buenrostro-bernstein:SS-LS_41_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:42.614126+00:00",
"file_format": "fastq",
"file_size": 1155308750,
"href": "/sequence-files/IGVFFI0003RJLQ/@@download/IGVFFI0003RJLQ.fastq.gz",
"md5sum": "4da56b2ad865db033b9b0eb23d5137e9",
"s3_uri": "s3://igvf-files/2023/09/05/00ce5034-6321-4a9a-be46-88f1b8b9f46f/IGVFFI0003RJLQ.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-156_L1_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9218BUCK/",
"accession": "IGVFFI9218BUCK",
"aliases": [
"bradley-bernstein:SS-LS_2031_R1",
"bradley-bernstein:SS-LS_241_R1",
"buenrostro-bernstein:SS-LS_2031_R1",
"buenrostro-bernstein:SS-LS_241_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:52.793771+00:00",
"file_format": "fastq",
"file_size": 639397359,
"href": "/sequence-files/IGVFFI9218BUCK/@@download/IGVFFI9218BUCK.fastq.gz",
"md5sum": "a129735879eb0cfa215ff71fc4ae705d",
"s3_uri": "s3://igvf-files/2023/09/05/20a8bf41-cdc4-489c-959c-c9d45565192a/IGVFFI9218BUCK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-156_L2_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1801NWGU/",
"accession": "IGVFFI1801NWGU",
"aliases": [
"bradley-bernstein:SS-LS_2031_R2",
"bradley-bernstein:SS-LS_241_R2",
"buenrostro-bernstein:SS-LS_2031_R2",
"buenrostro-bernstein:SS-LS_241_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2023-09-05T19:27:53.675223+00:00",
"file_format": "fastq",
"file_size": 1153386356,
"href": "/sequence-files/IGVFFI1801NWGU/@@download/IGVFFI1801NWGU.fastq.gz",
"md5sum": "e57e74bff2b5d78d46dc6dcb84709e35",
"s3_uri": "s3://igvf-files/2023/09/05/6045d14d-211c-4ca5-aa57-e0f33784d331/IGVFFI1801NWGU.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-156_L2_SS-PKR-129_2022-APRIL-R1-PLATE2-ENTIRE-PLATE_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI9086WGIT/",
"accession": "IGVFFI9086WGIT",
"aliases": [
"bradley-bernstein:SS-LS_2003_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:58.164100+00:00",
"file_format": "yaml",
"file_size": 1189,
"href": "/configuration-files/IGVFFI9086WGIT/@@download/IGVFFI9086WGIT.yaml.gz",
"md5sum": "fecd354efde6a22a9446fcfbd524e0e0",
"s3_uri": "s3://igvf-files/2024/09/17/cb6cda83-46c5-4160-8381-862845d2a342/IGVFFI9086WGIT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2003_seqspecv3.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7473ZEJG/",
"accession": "IGVFFI7473ZEJG",
"aliases": [
"bradley-bernstein:SS-LS_2031_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2024-09-17T22:49:51.539590+00:00",
"file_format": "yaml",
"file_size": 1187,
"href": "/configuration-files/IGVFFI7473ZEJG/@@download/IGVFFI7473ZEJG.yaml.gz",
"md5sum": "c250cb32623a7370413e052f26e9857f",
"s3_uri": "s3://igvf-files/2024/09/17/25755410-74dc-4c82-8e8f-fc4ec9c520d9/IGVFFI7473ZEJG.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/SS-LS_2031_seqspecv3.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8415FVDT/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 6,
"notes": "Preferred_assay_titles enum SHARE-Seq has been renamed to be SHARE-seq.",
"onlist_files": [
"/tabular-files/IGVFFI0400MBIM/"
],
"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/IGVFDS5192VPKQ/",
"accession": "IGVFDS5192VPKQ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS4911ZDCJ/",
"accession": "IGVFDS4911ZDCJ",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8535JZRF/",
"accession": "IGVFDS8535JZRF",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS3638UVNV/",
"accession": "IGVFDS3638UVNV",
"status": "released"
},
{
"@id": "/measurement-sets/IGVFDS8078FJZR/",
"accession": "IGVFDS8078FJZR",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:30.139354+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM3932SXVT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM3932SXVT",
"aliases": [
"bradley-bernstein:BioSam 4561_SS-PKR 129",
"buenrostro-bernstein:BioSam 4561_SS-PKR 129"
],
"cellular_sub_pool": "SS-PKR 129",
"classifications": [
"tissue"
],
"institutional_certificates": [],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0000955/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "released",
"summary": "brain",
"term_name": "brain"
}
],
"status": "released",
"summary": "Mus musculus C57BL/6 (female) brain tissue (cellular sub pool: SS-PKR 129)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2023-09-01T20:25:55.381680+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "34712787-4ba1-4cb7-baa4-afbadb5a5970"
}