{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4174PVSF/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4174PVSF",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1774"
],
"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 [IGVFSM1137TONP](/tissues/IGVFSM1137TONP/) 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/IGVFSM1137TONP/"
},
{
"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 [IGVFDS4174PVSF](/measurement-sets/IGVFDS4174PVSF/) 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/IGVFDS4174PVSF/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4174PVSF](/measurement-sets/IGVFDS4174PVSF/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4174PVSF/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS4174PVSF](/measurement-sets/IGVFDS4174PVSF/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS4174PVSF/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS4174PVSF](/measurement-sets/IGVFDS4174PVSF/) 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/IGVFDS4174PVSF/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM1137TONP](/tissues/IGVFSM1137TONP/) 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/IGVFSM1137TONP/"
}
]
},
"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": "2025-03-05T15:33:58.604744+00:00",
"donors": [
{
"@id": "/rodent-donors/IGVFDO3508PMXX/",
"accession": "IGVFDO3508PMXX",
"aliases": [
"ali-mortazavi:768_B6J_10F",
"buenrostro-bernstein:Donor 2078"
],
"sex": "female",
"status": "released",
"strain_background": "C57BL/6J (B6)",
"taxa": "Mus musculus"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI7672KXIG/",
"accession": "IGVFFI7672KXIG",
"aliases": [
"buenrostro-bernstein:SS-LS_8369_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:03.296883+00:00",
"file_format": "fastq",
"file_size": 3876242661,
"href": "/sequence-files/IGVFFI7672KXIG/@@download/IGVFFI7672KXIG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/5a44e5dc-34f7-4f2a-97ff-3e683b7fea89/IGVFFI7672KXIG.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-2249_L4_SS-PKR-602_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6916HPCW/",
"accession": "IGVFFI6916HPCW",
"aliases": [
"buenrostro-bernstein:SS-LS_8379_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:23.653298+00:00",
"file_format": "fastq",
"file_size": 5350523617,
"href": "/sequence-files/IGVFFI6916HPCW/@@download/IGVFFI6916HPCW.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/262c7894-d743-4964-b832-b731f6f84f6b/IGVFFI6916HPCW.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2249_L5_SS-PKR-602_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0710FCLU/",
"accession": "IGVFFI0710FCLU",
"aliases": [
"buenrostro-bernstein:SS-LS_8389_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:42.911183+00:00",
"file_format": "fastq",
"file_size": 3871691897,
"href": "/sequence-files/IGVFFI0710FCLU/@@download/IGVFFI0710FCLU.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/a06f85d9-8124-432e-a358-b216134a9ace/IGVFFI0710FCLU.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-2249_L6_SS-PKR-602_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2874QLUX/",
"accession": "IGVFFI2874QLUX",
"aliases": [
"buenrostro-bernstein:SS-LS_8379_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:21.649733+00:00",
"file_format": "fastq",
"file_size": 3871179435,
"href": "/sequence-files/IGVFFI2874QLUX/@@download/IGVFFI2874QLUX.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/124ec678-9cee-45b8-9bba-941dd2871a03/IGVFFI2874QLUX.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-2249_L5_SS-PKR-602_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI3203MNLV/",
"accession": "IGVFFI3203MNLV",
"aliases": [
"buenrostro-bernstein:SS-LS_8369_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:04.969159+00:00",
"file_format": "fastq",
"file_size": 5393949819,
"href": "/sequence-files/IGVFFI3203MNLV/@@download/IGVFFI3203MNLV.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b60abd24-952e-4ac5-8534-a992357b0898/IGVFFI3203MNLV.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-2249_L4_SS-PKR-602_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI2467ELBY/",
"accession": "IGVFFI2467ELBY",
"aliases": [
"buenrostro-bernstein:SS-LS_8389_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:45.366632+00:00",
"file_format": "fastq",
"file_size": 5352062146,
"href": "/sequence-files/IGVFFI2467ELBY/@@download/IGVFFI2467ELBY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/67e7e072-5231-40c0-ac33-77af9bf91d7c/IGVFFI2467ELBY.fastq.gz",
"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "released",
"submitted_file_name": "gs://broad-epi-ss-lane-subsets/SS-CoPA-2249_L6_SS-PKR-602_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3468IMGQ/",
"accession": "IGVFFI3468IMGQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8379_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:07.260975+00:00",
"file_format": "yaml",
"file_size": 1252,
"href": "/configuration-files/IGVFFI3468IMGQ/@@download/IGVFFI3468IMGQ.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/6649e280-679d-424a-b6f5-58057840880c/IGVFFI3468IMGQ.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8379_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI4546PTOK/",
"accession": "IGVFFI4546PTOK",
"aliases": [
"buenrostro-bernstein:SS-LS_8389_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T20:00:19.499574+00:00",
"file_format": "yaml",
"file_size": 1252,
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"s3_uri": "s3://igvf-files/2025/03/07/4d5dcffe-bfb7-49b5-ac5b-4a53b2b8d35a/IGVFFI4546PTOK.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8389_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI5162JESN/",
"accession": "IGVFFI5162JESN",
"aliases": [
"buenrostro-bernstein:SS-LS_8369_seqspec"
],
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"creation_timestamp": "2025-03-07T19:59:54.973382+00:00",
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8369_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS4515XRXX/"
],
"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/IGVFDS1996CWLE/",
"accession": "IGVFDS1996CWLE",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:22:07.159869+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM1137TONP/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM1137TONP",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 602"
],
"cellular_sub_pool": "SS-PKR 602",
"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 602)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
"submitted_files_timestamp": "2025-03-05T15:54:03.296883+00:00",
"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "6c723a82-3d31-4e09-91e2-0464b5235a24"
}