{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9828TNJA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9828TNJA",
"aliases": [
"buenrostro-bernstein:scATAC Lib 1778"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002764/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-cell ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"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 [IGVFSM7652DCKY](/tissues/IGVFSM7652DCKY/) 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/IGVFSM7652DCKY/"
},
{
"category": "missing publication",
"detail": "Measurement set [IGVFDS9828TNJA](/measurement-sets/IGVFDS9828TNJA/) 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/IGVFDS9828TNJA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9828TNJA](/measurement-sets/IGVFDS9828TNJA/) has in progress subobject tabular file [IGVFFI2668ZFEB](/tabular-files/IGVFFI2668ZFEB/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9828TNJA/"
},
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9828TNJA](/measurement-sets/IGVFDS9828TNJA/) has in progress subobject tabular file [IGVFFI6680XCDT](/tabular-files/IGVFFI6680XCDT/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9828TNJA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS9828TNJA](/measurement-sets/IGVFDS9828TNJA/) 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/IGVFDS9828TNJA/"
}
],
"WARNING": [
{
"category": "missing age",
"detail": "Tissue [IGVFSM7652DCKY](/tissues/IGVFSM7652DCKY/) 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/IGVFSM7652DCKY/"
}
]
},
"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": "2025-03-05T15:34:00.627226+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/IGVFFI7740WFBQ/",
"accession": "IGVFFI7740WFBQ",
"aliases": [
"buenrostro-bernstein:SS-LS_8373_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:11.665297+00:00",
"file_format": "fastq",
"file_size": 6579595869,
"href": "/sequence-files/IGVFFI7740WFBQ/@@download/IGVFFI7740WFBQ.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/b5e19c73-f150-4b12-8771-b6ec64074255/IGVFFI7740WFBQ.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-2253_L4_SS-PKR-604_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI5162FOSE/",
"accession": "IGVFFI5162FOSE",
"aliases": [
"buenrostro-bernstein:SS-LS_8373_R1"
],
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"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:09.984809+00:00",
"file_format": "fastq",
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"href": "/sequence-files/IGVFFI5162FOSE/@@download/IGVFFI5162FOSE.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/8e86ec36-17d6-4e17-bd5a-50beb5ad083e/IGVFFI5162FOSE.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-2253_L4_SS-PKR-604_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9908WIUF/",
"accession": "IGVFFI9908WIUF",
"aliases": [
"buenrostro-bernstein:SS-LS_8393_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:53.246246+00:00",
"file_format": "fastq",
"file_size": 6598075164,
"href": "/sequence-files/IGVFFI9908WIUF/@@download/IGVFFI9908WIUF.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/371ef482-f8ad-480e-bb5e-2f829517bb5c/IGVFFI9908WIUF.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-2253_L6_SS-PKR-604_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI0114RXZY/",
"accession": "IGVFFI0114RXZY",
"aliases": [
"buenrostro-bernstein:SS-LS_8383_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:31.807489+00:00",
"file_format": "fastq",
"file_size": 6549307203,
"href": "/sequence-files/IGVFFI0114RXZY/@@download/IGVFFI0114RXZY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/4ea05900-15da-4bd7-aab3-fa8686f40a89/IGVFFI0114RXZY.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-2253_L5_SS-PKR-604_SS-V1-RIGHT-HALF_R2.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI9489JPOG/",
"accession": "IGVFFI9489JPOG",
"aliases": [
"buenrostro-bernstein:SS-LS_8383_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:30.058105+00:00",
"file_format": "fastq",
"file_size": 4735805463,
"href": "/sequence-files/IGVFFI9489JPOG/@@download/IGVFFI9489JPOG.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/95f15778-28ea-4f9b-ad28-a4d8f8c56963/IGVFFI9489JPOG.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-2253_L5_SS-PKR-604_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI6593YTVY/",
"accession": "IGVFFI6593YTVY",
"aliases": [
"buenrostro-bernstein:SS-LS_8393_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-05T15:54:51.066274+00:00",
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"file_size": 4766845068,
"href": "/sequence-files/IGVFFI6593YTVY/@@download/IGVFFI6593YTVY.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/05/46235d0a-c49a-4dfe-a3d2-2c65ae5c30da/IGVFFI6593YTVY.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-2253_L6_SS-PKR-604_SS-V1-RIGHT-HALF_R1.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI3405IABA/",
"accession": "IGVFFI3405IABA",
"aliases": [
"buenrostro-bernstein:SS-LS_8373_seqspec"
],
"content_type": "seqspec",
"creation_timestamp": "2025-03-07T19:59:58.730426+00:00",
"file_format": "yaml",
"file_size": 1249,
"href": "/configuration-files/IGVFFI3405IABA/@@download/IGVFFI3405IABA.yaml.gz",
"s3_uri": "s3://igvf-files/2025/03/07/8f91022d-e5de-4421-bb6e-a1299bff15b0/IGVFFI3405IABA.yaml.gz",
"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8373_seqspec.yaml.gz",
"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI6218QCFR/",
"accession": "IGVFFI6218QCFR",
"aliases": [
"buenrostro-bernstein:SS-LS_8383_seqspec"
],
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"creation_timestamp": "2025-03-07T20:00:12.951696+00:00",
"file_format": "yaml",
"file_size": 1250,
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"s3_uri": "s3://igvf-files/2025/03/07/2578b8c1-441e-4074-8a38-4e074c0c7bae/IGVFFI6218QCFR.yaml.gz",
"status": "released",
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"upload_status": "validated"
},
{
"@id": "/configuration-files/IGVFFI0613UHRD/",
"accession": "IGVFFI0613UHRD",
"aliases": [
"buenrostro-bernstein:SS-LS_8393_seqspec"
],
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"status": "released",
"submitted_file_name": "gs://sw-igvf-submission/seqspec-v3/mouse-bridge/SS-LS_8393_seqspec.yaml.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS7635YNBH/"
],
"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/IGVFDS3074DPDQ/",
"accession": "IGVFDS3074DPDQ",
"status": "released"
}
],
"release_timestamp": "2025-03-28T21:17:39.376606+00:00",
"samples": [
{
"@id": "/tissues/IGVFSM7652DCKY/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM7652DCKY",
"aliases": [
"buenrostro-bernstein:BioSam 5155_SS-PKR 604"
],
"cellular_sub_pool": "SS-PKR 604",
"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 604)",
"taxa": "Mus musculus"
}
],
"schema_version": "26",
"status": "released",
"submitted_by": {
"@id": "/users/c0838247-5022-46cf-a8fa-426e73bf4c94/",
"title": "Siddarth Wekhande"
},
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"summary": "single-cell ATAC-seq (SHARE-seq)",
"uuid": "42c3cb8b-6db5-49a1-b5ca-d51f9abea62d"
}