{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0512QYBW/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0512QYBW",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1480"
],
"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 [IGVFDS0512QYBW](/measurement-sets/IGVFDS0512QYBW/) 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/IGVFDS0512QYBW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0512QYBW](/measurement-sets/IGVFDS0512QYBW/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0512QYBW/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS0512QYBW](/measurement-sets/IGVFDS0512QYBW/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS0512QYBW/"
},
{
"category": "missing publication",
"detail": "Tissue [IGVFSM6459ANYG](/tissues/IGVFSM6459ANYG/) 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/IGVFSM6459ANYG/"
},
{
"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/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS0512QYBW](/measurement-sets/IGVFDS0512QYBW/) 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/IGVFDS0512QYBW/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM6459ANYG](/tissues/IGVFSM6459ANYG/) 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/IGVFSM6459ANYG/"
}
]
},
"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": "2025-03-05T15:33:36.274787+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/IGVFFI5419VJUK/",
"accession": "IGVFFI5419VJUK",
"aliases": [
"buenrostro-bernstein:SS-LS_7390_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:46.383335+00:00",
"file_format": "fastq",
"file_size": 8777219698,
"href": "/sequence-files/IGVFFI5419VJUK/@@download/IGVFFI5419VJUK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f26dc093-9ef7-45ab-8ccc-d73d9aaa3b31/IGVFFI5419VJUK.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-1951_L2_SS-PKR-502_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6874DKSO/",
"accession": "IGVFFI6874DKSO",
"aliases": [
"buenrostro-bernstein:SS-LS_7390_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:44.263517+00:00",
"file_format": "fastq",
"file_size": 5795588778,
"href": "/sequence-files/IGVFFI6874DKSO/@@download/IGVFFI6874DKSO.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/f3f5bf18-ae6c-4d48-bc41-ef8e4a26caa7/IGVFFI6874DKSO.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-1951_L2_SS-PKR-502_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3985UALS/",
"accession": "IGVFFI3985UALS",
"aliases": [
"buenrostro-bernstein:SS-LS_7384_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:33.262381+00:00",
"file_format": "fastq",
"file_size": 8816479524,
"href": "/sequence-files/IGVFFI3985UALS/@@download/IGVFFI3985UALS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/6d34c66b-803f-4b4b-bbb1-c00e50969737/IGVFFI3985UALS.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-1951_L1_SS-PKR-502_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4966LYYA/",
"accession": "IGVFFI4966LYYA",
"aliases": [
"buenrostro-bernstein:SS-LS_7384_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:51:30.891057+00:00",
"file_format": "fastq",
"file_size": 5867084543,
"href": "/sequence-files/IGVFFI4966LYYA/@@download/IGVFFI4966LYYA.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/2575e73b-65d1-47fd-bc1e-e552631b2e24/IGVFFI4966LYYA.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-1951_L1_SS-PKR-502_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI2979POWY/",
"accession": "IGVFFI2979POWY",
"aliases": [
"buenrostro-bernstein:SS-LS_7390_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:19.819570+00:00",
"file_format": "yaml",
"file_size": 1250,
"href": "/configuration-files/IGVFFI2979POWY/@@download/IGVFFI2979POWY.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/ae80664a-df87-40a7-8852-206f4b838497/IGVFFI2979POWY.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7390_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI8675KOSR/",
"accession": "IGVFFI8675KOSR",
"aliases": [
"buenrostro-bernstein:SS-LS_7384_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:13.090398+00:00",
"file_format": "yaml",
"file_size": 1251,
"href": "/configuration-files/IGVFFI8675KOSR/@@download/IGVFFI8675KOSR.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/ab5b0258-327f-4f6d-b110-e2e3f0cd72f7/IGVFFI8675KOSR.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_7384_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS3628FWPB/"
],
"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/IGVFDS7100QYTS/",
"accession": "IGVFDS7100QYTS",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:18:28.349207+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM6459ANYG/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM6459ANYG",
"aliases": [
"buenrostro-bernstein:BioSam 5153_SS-PKR 502"
],
"cellular_sub_pool": "SS-PKR 502",
"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 502)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:51:30.891057+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "4a1eea0e-c246-4b1b-a559-ca940dff3466"
}