{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9836XZJI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9836XZJI",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1483"
],
"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 [IGVFDS9836XZJI](/measurement-sets/IGVFDS9836XZJI/) 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/IGVFDS9836XZJI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9836XZJI](/measurement-sets/IGVFDS9836XZJI/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9836XZJI/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9836XZJI](/measurement-sets/IGVFDS9836XZJI/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9836XZJI/"
},
{
"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": "Tissue [IGVFSM9232VQYX](/tissues/IGVFSM9232VQYX/) 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/IGVFSM9232VQYX/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9836XZJI](/measurement-sets/IGVFDS9836XZJI/) 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/IGVFDS9836XZJI/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM9232VQYX](/tissues/IGVFSM9232VQYX/) 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/IGVFSM9232VQYX/"
}
]
},
"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": "2025-03-05T15:34:12.029519+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/IGVFFI6431CIVH/",
"accession": "IGVFFI6431CIVH",
"aliases": [
"buenrostro-bernstein:SS-LS_7388_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:26.590796+00:00",
"file_format": "fastq",
"file_size": 5874192389,
"href": "/sequence-files/IGVFFI6431CIVH/@@download/IGVFFI6431CIVH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/8eee63f0-3b58-4580-88d4-8791b94bd15b/IGVFFI6431CIVH.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-1954_L2_SS-PKR-503_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5100XZJS/",
"accession": "IGVFFI5100XZJS",
"aliases": [
"buenrostro-bernstein:SS-LS_7382_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:14.649267+00:00",
"file_format": "fastq",
"file_size": 8953521408,
"href": "/sequence-files/IGVFFI5100XZJS/@@download/IGVFFI5100XZJS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/e5878ee7-d832-485d-8b71-95dacb510dc6/IGVFFI5100XZJS.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-1954_L1_SS-PKR-503_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2655ZCMP/",
"accession": "IGVFFI2655ZCMP",
"aliases": [
"buenrostro-bernstein:SS-LS_7382_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:12.613388+00:00",
"file_format": "fastq",
"file_size": 6072633487,
"href": "/sequence-files/IGVFFI2655ZCMP/@@download/IGVFFI2655ZCMP.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/d4ad9e3d-87aa-463e-98a2-40eb80075e1f/IGVFFI2655ZCMP.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-1954_L1_SS-PKR-503_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6851KIGV/",
"accession": "IGVFFI6851KIGV",
"aliases": [
"buenrostro-bernstein:SS-LS_7388_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:56:28.453624+00:00",
"file_format": "fastq",
"file_size": 8741728200,
"href": "/sequence-files/IGVFFI6851KIGV/@@download/IGVFFI6851KIGV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/97e9ac93-3898-40d3-82e5-bb58be9f1e54/IGVFFI6851KIGV.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-1954_L2_SS-PKR-503_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4792JCKV/",
"accession": "IGVFFI4792JCKV",
"aliases": [
"buenrostro-bernstein:SS-LS_7388_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:39.182018+00:00",
"file_format": "yaml",
"file_size": 1247,
"href": "/configuration-files/IGVFFI4792JCKV/@@download/IGVFFI4792JCKV.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/b86e1c89-b57d-4124-977f-8ed68b918a94/IGVFFI4792JCKV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7388_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0952ONSE/",
"accession": "IGVFFI0952ONSE",
"aliases": [
"buenrostro-bernstein:SS-LS_7382_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:33.909296+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI0952ONSE/@@download/IGVFFI0952ONSE.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/b9395d36-34bb-4ad3-a347-bb271413b447/IGVFFI0952ONSE.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7382_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS2822VFWB/"
],
"lab": {
"@id": "/labs/jason-buenrostro/",
"title": "Jason Buenrostro, Broad"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI3897QKNI/",
"/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/IGVFDS8953MKJE/",
"accession": "IGVFDS8953MKJE",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:58.964798+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM9232VQYX/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9232VQYX",
"aliases": [
"buenrostro-bernstein:BioSam 5150_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 CASTJ (male) 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": "2025-03-05T15:56:12.613388+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "c6f86a45-c87d-4bdc-9ad2-7b6754e3dbe7"
}