{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8487QXIK/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8487QXIK",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1482"
],
"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 [IGVFSM4419MRHA](/tissues/IGVFSM4419MRHA/) 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/IGVFSM4419MRHA/"
},
{
"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 [IGVFDS8487QXIK](/measurement-sets/IGVFDS8487QXIK/) 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/IGVFDS8487QXIK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8487QXIK](/measurement-sets/IGVFDS8487QXIK/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8487QXIK/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS8487QXIK](/measurement-sets/IGVFDS8487QXIK/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS8487QXIK/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS8487QXIK](/measurement-sets/IGVFDS8487QXIK/) 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/IGVFDS8487QXIK/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM4419MRHA](/tissues/IGVFSM4419MRHA/) 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/IGVFSM4419MRHA/"
}
]
},
"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": "2025-03-05T15:33:34.905775+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO7484YDXT/",
"accession": "IGVFDO7484YDXT",
"aliases": [
"ali-mortazavi:766_B6J_10F",
"buenrostro-bernstein:Donor 2076"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4773YQEF/",
"accession": "IGVFFI4773YQEF",
"aliases": [
"buenrostro-bernstein:SS-LS_7383_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:28.072244+00:00",
"file_format": "fastq",
"file_size": 6592128880,
"href": "/sequence-files/IGVFFI4773YQEF/@@download/IGVFFI4773YQEF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6af298fe-855b-4e37-89fe-4b285453699b/IGVFFI4773YQEF.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-1953_L1_SS-PKR-503_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6103IWOF/",
"accession": "IGVFFI6103IWOF",
"aliases": [
"buenrostro-bernstein:SS-LS_7389_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:40.398972+00:00",
"file_format": "fastq",
"file_size": 4325471138,
"href": "/sequence-files/IGVFFI6103IWOF/@@download/IGVFFI6103IWOF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d43c6bfd-de1c-4935-91ff-045d535f3243/IGVFFI6103IWOF.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-1953_L2_SS-PKR-503_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7241VYRQ/",
"accession": "IGVFFI7241VYRQ",
"aliases": [
"buenrostro-bernstein:SS-LS_7389_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:42.498725+00:00",
"file_format": "fastq",
"file_size": 6410449863,
"href": "/sequence-files/IGVFFI7241VYRQ/@@download/IGVFFI7241VYRQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/28313596-5b2a-4c3a-8962-af98ae7d3403/IGVFFI7241VYRQ.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-1953_L2_SS-PKR-503_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI1918YZDJ/",
"accession": "IGVFFI1918YZDJ",
"aliases": [
"buenrostro-bernstein:SS-LS_7383_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:25.340619+00:00",
"file_format": "fastq",
"file_size": 4488812422,
"href": "/sequence-files/IGVFFI1918YZDJ/@@download/IGVFFI1918YZDJ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/1f72f0c1-b94d-45dc-841c-93436aa6a80d/IGVFFI1918YZDJ.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-1953_L1_SS-PKR-503_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6641GKMT/",
"accession": "IGVFFI6641GKMT",
"aliases": [
"buenrostro-bernstein:SS-LS_7389_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:17.244703+00:00",
"file_format": "yaml",
"file_size": 1252,
"href": "/configuration-files/IGVFFI6641GKMT/@@download/IGVFFI6641GKMT.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/bb020fcd-827b-44a5-87a9-d015228ed7de/IGVFFI6641GKMT.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7389_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8012OCZQ/",
"accession": "IGVFFI8012OCZQ",
"aliases": [
"buenrostro-bernstein:SS-LS_7383_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:11.165352+00:00",
"file_format": "yaml",
"file_size": 1253,
"href": "/configuration-files/IGVFFI8012OCZQ/@@download/IGVFFI8012OCZQ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/1ae247e0-ace3-4167-920a-30e49a13cef5/IGVFFI8012OCZQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7383_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS0657NHTA/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI6680XCDT/",
"/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/IGVFDS6617HQDI/",
"accession": "IGVFDS6617HQDI",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:43.089392+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM4419MRHA/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM4419MRHA",
"aliases": [
"buenrostro-bernstein:BioSam 5153_SS-PKR 503"
],
"cellular_sub_pool": "SS-PKR 503",
"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 C57BL/6J (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 503)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:51:25.340619+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "2cc5c619-0f94-4c3a-8642-733686ca3bf5"
}