{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9519NBWN/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9519NBWN",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1476"
],
"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 [IGVFSM6189KRRN](/tissues/IGVFSM6189KRRN/) 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/IGVFSM6189KRRN/"
},
{
"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 [IGVFDS9519NBWN](/measurement-sets/IGVFDS9519NBWN/) 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/IGVFDS9519NBWN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9519NBWN](/measurement-sets/IGVFDS9519NBWN/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9519NBWN/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9519NBWN](/measurement-sets/IGVFDS9519NBWN/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9519NBWN/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9519NBWN](/measurement-sets/IGVFDS9519NBWN/) 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/IGVFDS9519NBWN/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6189KRRN](/tissues/IGVFSM6189KRRN/) 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/IGVFSM6189KRRN/"
}
]
},
"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": "2025-03-05T15:33:37.541000+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/IGVFFI9298RECV/",
"accession": "IGVFFI9298RECV",
"aliases": [
"buenrostro-bernstein:SS-LS_7385_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:38.442644+00:00",
"file_format": "fastq",
"file_size": 8066571184,
"href": "/sequence-files/IGVFFI9298RECV/@@download/IGVFFI9298RECV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/fe3ee72a-3423-470a-803a-ba499476898a/IGVFFI9298RECV.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-1949_L1_SS-PKR-500_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9204ZDZC/",
"accession": "IGVFFI9204ZDZC",
"aliases": [
"buenrostro-bernstein:SS-LS_7391_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:51.565288+00:00",
"file_format": "fastq",
"file_size": 7824205507,
"href": "/sequence-files/IGVFFI9204ZDZC/@@download/IGVFFI9204ZDZC.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/156568dc-79a4-46b5-bf60-878e28bc5057/IGVFFI9204ZDZC.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-1949_L2_SS-PKR-500_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6975MWYL/",
"accession": "IGVFFI6975MWYL",
"aliases": [
"buenrostro-bernstein:SS-LS_7385_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:35.185219+00:00",
"file_format": "fastq",
"file_size": 5495419636,
"href": "/sequence-files/IGVFFI6975MWYL/@@download/IGVFFI6975MWYL.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/665c43ad-085b-42f9-8e57-4a2ede3cf71f/IGVFFI6975MWYL.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-1949_L1_SS-PKR-500_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3853SHJH/",
"accession": "IGVFFI3853SHJH",
"aliases": [
"buenrostro-bernstein:SS-LS_7391_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:48.788801+00:00",
"file_format": "fastq",
"file_size": 5285595830,
"href": "/sequence-files/IGVFFI3853SHJH/@@download/IGVFFI3853SHJH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a4ccfecb-37c8-445a-b596-514aa53e7f02/IGVFFI3853SHJH.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-1949_L2_SS-PKR-500_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3174UVJI/",
"accession": "IGVFFI3174UVJI",
"aliases": [
"buenrostro-bernstein:SS-LS_7385_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:15.447607+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI3174UVJI/@@download/IGVFFI3174UVJI.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/d3fa10e8-6c7a-4825-825e-15ff7ce8a2a7/IGVFFI3174UVJI.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7385_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4352WWYD/",
"accession": "IGVFFI4352WWYD",
"aliases": [
"buenrostro-bernstein:SS-LS_7391_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:21.755148+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI4352WWYD/@@download/IGVFFI4352WWYD.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/64d27040-c273-4a12-b5fb-bbdfd849d609/IGVFFI4352WWYD.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7391_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8609VYFV/"
],
"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/IGVFDS4731ODMK/",
"accession": "IGVFDS4731ODMK",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:21:56.922646+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6189KRRN/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6189KRRN",
"aliases": [
"buenrostro-bernstein:BioSam 5153_SS-PKR 500"
],
"cellular_sub_pool": "SS-PKR 500",
"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 500)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:51:35.185219+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "9a070a8f-0a1b-4cd1-bb9e-37d623c6b1e9"
}