{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS3515HEZA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS3515HEZA",
"aliases": [
"igvf:corces_measurementSet_X008_G1_ATAC"
],
"assay_term": {
"@id": "/assay-terms/OBI_0002762/",
"assay_slims": [
"chromatin accessibility"
],
"status": "released",
"term_name": "single-nucleus ATAC-seq"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Preview tissue [IGVFSM5610ZMIM](/tissues/IGVFSM5610ZMIM/) has in progress subobject phenotype term [DOID_14330](/phenotype-terms/DOID_14330/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/tissues/IGVFSM5610ZMIM/"
},
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM5610ZMIM](/tissues/IGVFSM5610ZMIM/) is missing a `ccf_id`. Human tissues are expected to specify a common coordinate framework identifier (CCF ID).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_tissue_ccf_id",
"path": "/tissues/IGVFSM5610ZMIM/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [7a3d9384-554b-480b-b1f3-41a99dd54465](/phenotypic-features/7a3d9384-554b-480b-b1f3-41a99dd54465/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4108VCBA/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [f32d310f-3150-421e-9656-a5fbaf04eebd](/phenotypic-features/f32d310f-3150-421e-9656-a5fbaf04eebd/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4108VCBA/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [956b5474-2acd-4c13-bbc1-dd81dba0622a](/phenotypic-features/956b5474-2acd-4c13-bbc1-dd81dba0622a/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4108VCBA/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [d2909f2d-5e28-4e1f-859d-c562f1c883af](/phenotypic-features/d2909f2d-5e28-4e1f-859d-c562f1c883af/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4108VCBA/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [1bb96444-071d-4a8d-81ef-b6567ef83275](/phenotypic-features/1bb96444-071d-4a8d-81ef-b6567ef83275/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4108VCBA/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO4108VCBA](/human-donors/IGVFDO4108VCBA/) has in progress subobject phenotypic feature [aff60c46-5191-4203-ac06-8623d7e676fa](/phenotypic-features/aff60c46-5191-4203-ac06-8623d7e676fa/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO4108VCBA/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS3515HEZA](/measurement-sets/IGVFDS3515HEZA/) has sequence file(s): [IGVFFI4127WXZS](/sequence-files/IGVFFI4127WXZS/), [IGVFFI4582UMYM](/sequence-files/IGVFFI4582UMYM/), [IGVFFI8190LVYH](/sequence-files/IGVFFI8190LVYH/), [IGVFFI8798WMRK](/sequence-files/IGVFFI8798WMRK/) which do not have any `seqspecs`. Sequence files in a file set associated with single cell data are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS3515HEZA/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS3515HEZA](/measurement-sets/IGVFDS3515HEZA/) 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/IGVFDS3515HEZA/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS3515HEZA](/measurement-sets/IGVFDS3515HEZA/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
"level": 40,
"level_name": "WARNING",
"name": "audit_input_for",
"path": "/measurement-sets/IGVFDS3515HEZA/"
}
]
},
"award": {
"@id": "/awards/HG012076/",
"component": "mapping",
"contact_pi": {
"@id": "/users/eae4c275-1e07-45e4-ae67-3e437a8680bb/",
"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
"control_for": [],
"controlled_access": false,
"creation_timestamp": "2025-03-19T19:11:18.145019+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO4108VCBA/",
"accession": "IGVFDO4108VCBA",
"aliases": [
"igvf:corces_donor_BANN0325"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4127WXZS/",
"accession": "IGVFFI4127WXZS",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X008_G1_P005_L001_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:41:37.466602+00:00",
"file_format": "fastq",
"file_size": 16653690169,
"href": "/sequence-files/IGVFFI4127WXZS/@@download/IGVFFI4127WXZS.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/20/7f245e69-b0e1-437d-b2a8-f6a4c41b2561/IGVFFI4127WXZS.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_03-25_SN_X008_L001_B1_T1_P005_S9_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI4582UMYM/",
"accession": "IGVFFI4582UMYM",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X008_G1_P005_L001_R3"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:41:40.366244+00:00",
"file_format": "fastq",
"file_size": 17249626946,
"href": "/sequence-files/IGVFFI4582UMYM/@@download/IGVFFI4582UMYM.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/20/80fbac77-59fc-4087-8260-0c8955c93563/IGVFFI4582UMYM.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_03-25_SN_X008_L001_B1_T1_P005_S9_L001_R3_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8190LVYH/",
"accession": "IGVFFI8190LVYH",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X008_G1_P005_L001_I1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:41:35.969683+00:00",
"file_format": "fastq",
"file_size": 2422870002,
"href": "/sequence-files/IGVFFI8190LVYH/@@download/IGVFFI8190LVYH.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/20/23fdafbd-4d55-4820-bfd5-953e5c4d66b4/IGVFFI8190LVYH.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_03-25_SN_X008_L001_B1_T1_P005_S9_L001_I1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8798WMRK/",
"accession": "IGVFFI8798WMRK",
"aliases": [
"igvf:corces_sequenceFile_ATAC_X008_G1_P005_L001_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:41:38.905337+00:00",
"file_format": "fastq",
"file_size": 5774079021,
"href": "/sequence-files/IGVFFI8798WMRK/@@download/IGVFFI8798WMRK.fastq.gz",
"s3_uri": "s3://igvf-files/2025/03/20/0408f4cb-2cbb-4ebf-b7d2-bde20a0d523d/IGVFFI8798WMRK.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_ATAC_PD_03-25_SN_X008_L001_B1_T1_P005_S9_L001_R2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [],
"lab": {
"@id": "/labs/ryan-corces/",
"title": "Ryan Corces, Gladstone Institute UCSF"
},
"multiome_size": 2,
"onlist_files": [
"/tabular-files/IGVFFI7587TJLC/"
],
"onlist_method": "no combination",
"preferred_assay_title": "10x multiome",
"protocols": [
"https://www.protocols.io/view/chromium-next-gem-single-cell-multiome-atac-gene-e-d5k784zn"
],
"related_multiome_datasets": [
{
"@id": "/measurement-sets/IGVFDS9811IRQC/",
"accession": "IGVFDS9811IRQC",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM5610ZMIM/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM5610ZMIM",
"aliases": [
"igvf:corces_tissue_BANN0325_SN_B1-singleplex"
],
"classifications": [
"tissue"
],
"disease_terms": [
{
"@id": "/phenotype-terms/DOID_14330/",
"status": "in progress",
"term_name": "Parkinson's disease"
}
],
"institutional_certificates": [
{
"@id": "/institutional-certificates/f7742e0d-bba4-4ca3-ab80-71c7364f24e7/",
"certificate_identifier": "IP115-05",
"controlled_access": false,
"status": "in progress"
}
],
"sample_terms": [
{
"@id": "/sample-terms/UBERON_0002038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "substantia nigra",
"term_name": "substantia nigra"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 78 years) substantia nigra tissue associated with Parkinson's disease",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-20T00:41:35.969683+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "98b5ca2a-8c18-42d4-bf19-2d38e0357a33"
}