{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4736GQFE/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4736GQFE",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1706"
],
"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 [IGVFSM6228EUYU](/tissues/IGVFSM6228EUYU/) 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/IGVFSM6228EUYU/"
},
{
"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 [IGVFDS4736GQFE](/measurement-sets/IGVFDS4736GQFE/) 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/IGVFDS4736GQFE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4736GQFE](/measurement-sets/IGVFDS4736GQFE/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4736GQFE/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4736GQFE](/measurement-sets/IGVFDS4736GQFE/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4736GQFE/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4736GQFE](/measurement-sets/IGVFDS4736GQFE/) 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/IGVFDS4736GQFE/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6228EUYU](/tissues/IGVFSM6228EUYU/) 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/IGVFSM6228EUYU/"
}
]
},
"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": "2025-03-05T17:52:38.365158+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO4657FUEV/",
"accession": "IGVFDO4657FUEV",
"aliases": [
"ali-mortazavi:771_B6J_10M",
"buenrostro-bernstein:Donor 2077"
],
"sex": "male",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI1240NFHV/",
"accession": "IGVFFI1240NFHV",
"aliases": [
"buenrostro-bernstein:SS-LS_8319_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:31.748331+00:00",
"file_format": "fastq",
"file_size": 3694337539,
"href": "/sequence-files/IGVFFI1240NFHV/@@download/IGVFFI1240NFHV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/130c20f6-a86c-4214-9786-f3e3a8534474/IGVFFI1240NFHV.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-2165_L1_SS-PKR-584_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0045DPKF/",
"accession": "IGVFFI0045DPKF",
"aliases": [
"buenrostro-bernstein:SS-LS_8319_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:57:33.251965+00:00",
"file_format": "fastq",
"file_size": 5163068648,
"href": "/sequence-files/IGVFFI0045DPKF/@@download/IGVFFI0045DPKF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4a64e560-b04e-4732-866e-b764f9c2126f/IGVFFI0045DPKF.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-2165_L1_SS-PKR-584_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7188XXIH/",
"accession": "IGVFFI7188XXIH",
"aliases": [
"buenrostro-bernstein:SS-LS_8351_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:02.147540+00:00",
"file_format": "fastq",
"file_size": 1920770486,
"href": "/sequence-files/IGVFFI7188XXIH/@@download/IGVFFI7188XXIH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/88ed9483-f835-4bf6-92bf-cd04643b632b/IGVFFI7188XXIH.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-2237_L8_SS-PKR-584_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3484UBVB/",
"accession": "IGVFFI3484UBVB",
"aliases": [
"buenrostro-bernstein:SS-LS_8351_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T17:58:00.738122+00:00",
"file_format": "fastq",
"file_size": 1360779782,
"href": "/sequence-files/IGVFFI3484UBVB/@@download/IGVFFI3484UBVB.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/69413724-8f91-41b8-8ac4-57724b129cea/IGVFFI3484UBVB.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-2237_L8_SS-PKR-584_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2725HAQV/",
"accession": "IGVFFI2725HAQV",
"aliases": [
"buenrostro-bernstein:SS-LS_8319_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:36.759146+00:00",
"file_format": "yaml",
"file_size": 1252,
"href": "/configuration-files/IGVFFI2725HAQV/@@download/IGVFFI2725HAQV.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/9fa52984-817d-402a-bf5e-be33bf84b8da/IGVFFI2725HAQV.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8319_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8926OWOZ/",
"accession": "IGVFFI8926OWOZ",
"aliases": [
"buenrostro-bernstein:SS-LS_8351_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:53.124404+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI8926OWOZ/@@download/IGVFFI8926OWOZ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/c1751edc-5c75-46fd-8146-73e672a9ec30/IGVFFI8926OWOZ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8351_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4904NBTM/"
],
"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/IGVFDS0131VONY/",
"accession": "IGVFDS0131VONY",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:37.604586+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6228EUYU/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6228EUYU",
"aliases": [
"buenrostro-bernstein:BioSam 5154_SS-PKR 584"
],
"cellular_sub_pool": "SS-PKR 584",
"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 B6J (male) left cerebral cortex tissue (cellular sub pool: SS-PKR 584)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T17:57:31.748331+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "8e98cb0b-89db-4705-930f-b4a03bf29b69"
}