{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7911YQZW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7911YQZW",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1556"
],
"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 [IGVFDS7911YQZW](/measurement-sets/IGVFDS7911YQZW/) 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/IGVFDS7911YQZW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7911YQZW](/measurement-sets/IGVFDS7911YQZW/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7911YQZW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS7911YQZW](/measurement-sets/IGVFDS7911YQZW/) has in progress subobject tabular file [IGVFFI3897QKNI](/tabular-files/IGVFFI3897QKNI/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS7911YQZW/"
},
{
"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 [IGVFSM1072XOVT](/tissues/IGVFSM1072XOVT/) 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/IGVFSM1072XOVT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7911YQZW](/measurement-sets/IGVFDS7911YQZW/) 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/IGVFDS7911YQZW/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1072XOVT](/tissues/IGVFSM1072XOVT/) 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/IGVFSM1072XOVT/"
}
]
},
"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": "2025-03-05T15:34:21.782637+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO2374RRPN/",
"accession": "IGVFDO2374RRPN",
"aliases": [
"ali-mortazavi:772_CASTJ_10F",
"buenrostro-bernstein:Donor 2074"
],
"sex": "female",
"status": "released",
"strain_background": "CAST/EiJ (CAST)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7137LDOI/",
"accession": "IGVFFI7137LDOI",
"aliases": [
"buenrostro-bernstein:SS-LS_8343_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:23.776578+00:00",
"file_format": "fastq",
"file_size": 3110675038,
"href": "/sequence-files/IGVFFI7137LDOI/@@download/IGVFFI7137LDOI.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/54809393-4189-4a2b-b005-c7bd1681f957/IGVFFI7137LDOI.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-2229_L8_SS-PKR-533_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4548IMBD/",
"accession": "IGVFFI4548IMBD",
"aliases": [
"buenrostro-bernstein:SS-LS_8279_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:11.773219+00:00",
"file_format": "fastq",
"file_size": 4855643471,
"href": "/sequence-files/IGVFFI4548IMBD/@@download/IGVFFI4548IMBD.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/cac0e8e4-ba1f-4d5a-a284-a942d93d27c8/IGVFFI4548IMBD.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-2157_L2_SS-PKR-533_SS-V1-LEFT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6905GFET/",
"accession": "IGVFFI6905GFET",
"aliases": [
"buenrostro-bernstein:SS-LS_8343_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:58:26.030122+00:00",
"file_format": "fastq",
"file_size": 4398172859,
"href": "/sequence-files/IGVFFI6905GFET/@@download/IGVFFI6905GFET.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/02d020f0-51f9-4d0c-b9a5-abd3f72223b1/IGVFFI6905GFET.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-2229_L8_SS-PKR-533_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9183WJEW/",
"accession": "IGVFFI9183WJEW",
"aliases": [
"buenrostro-bernstein:SS-LS_8279_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:57:13.590904+00:00",
"file_format": "fastq",
"file_size": 6882235739,
"href": "/sequence-files/IGVFFI9183WJEW/@@download/IGVFFI9183WJEW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/e2fe535f-bc24-4d6d-9cb0-038e74f5ead6/IGVFFI9183WJEW.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-2157_L2_SS-PKR-533_SS-V1-LEFT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI7926CEIJ/",
"accession": "IGVFFI7926CEIJ",
"aliases": [
"buenrostro-bernstein:SS-LS_8343_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:01:03.961974+00:00",
"file_format": "yaml",
"file_size": 1249,
"href": "/configuration-files/IGVFFI7926CEIJ/@@download/IGVFFI7926CEIJ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/c70a4ea5-f00f-47ae-846f-6978e80a455a/IGVFFI7926CEIJ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8343_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6672DITW/",
"accession": "IGVFFI6672DITW",
"aliases": [
"buenrostro-bernstein:SS-LS_8279_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:48.601293+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI6672DITW/@@download/IGVFFI6672DITW.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/e3a716d3-4b4d-451b-8894-a08cae07a72d/IGVFFI6672DITW.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8279_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8871DRGI/"
],
"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/IGVFDS4886GWPA/",
"accession": "IGVFDS4886GWPA",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:16.515829+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1072XOVT/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1072XOVT",
"aliases": [
"buenrostro-bernstein:BioSam 5151_SS-PKR 533"
],
"cellular_sub_pool": "SS-PKR 533",
"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 (female) left cerebral cortex tissue (cellular sub pool: SS-PKR 533)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:57:11.773219+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "622ad777-df70-4ce3-8ee4-fa5fe9281894"
}