{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5528ZTLH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5528ZTLH",
"aliases": [
"igvf:corces_measurementSet_X004_G3_RNA"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003109/",
"assay_slims": [
"gene expression"
],
"status": "released",
"term_name": "single-nucleus RNA sequencing assay"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing CCF ID",
"detail": "Tissue [IGVFSM9133DPZS](/tissues/IGVFSM9133DPZS/) 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/IGVFSM9133DPZS/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [3722891d-0d84-4ede-8520-3db83e7a6b16](/phenotypic-features/3722891d-0d84-4ede-8520-3db83e7a6b16/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [c0ce9b04-e7ed-4b93-a2eb-beb1600b8a07](/phenotypic-features/c0ce9b04-e7ed-4b93-a2eb-beb1600b8a07/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [45dc979b-555f-4b01-8d0f-a743d2314876](/phenotypic-features/45dc979b-555f-4b01-8d0f-a743d2314876/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [973e8365-f16f-4cd4-b8d8-3810cfb6de08](/phenotypic-features/973e8365-f16f-4cd4-b8d8-3810cfb6de08/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
},
{
"category": "mismatched status",
"detail": "Preview human donor [IGVFDO9236YUAT](/human-donors/IGVFDO9236YUAT/) has in progress subobject phenotypic feature [633b00ad-b194-4a5e-996f-0e6e7d188a4b](/phenotypic-features/633b00ad-b194-4a5e-996f-0e6e7d188a4b/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/human-donors/IGVFDO9236YUAT/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5528ZTLH](/measurement-sets/IGVFDS5528ZTLH/) has sequence file(s): [IGVFFI4079XVLD](/sequence-files/IGVFFI4079XVLD/), [IGVFFI7279RHVG](/sequence-files/IGVFFI7279RHVG/) 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/IGVFDS5528ZTLH/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS5528ZTLH](/measurement-sets/IGVFDS5528ZTLH/) 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/IGVFDS5528ZTLH/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS5528ZTLH](/measurement-sets/IGVFDS5528ZTLH/) 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/IGVFDS5528ZTLH/"
}
]
},
"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": "2025-03-19T19:11:22.675280+00:00",
"data_use_limitation_summaries": [
"No limitations"
],
"donors": [
{
"@id": "/human-donors/IGVFDO9236YUAT/",
"accession": "IGVFDO9236YUAT",
"aliases": [
"igvf:corces_donor_BANN0227"
],
"sex": "male",
"status": "preview",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
"files": [
{
"@id": "/sequence-files/IGVFFI4079XVLD/",
"accession": "IGVFFI4079XVLD",
"aliases": [
"igvf:corces_sequenceFile_RNA_X004_G3_P004_L001_R1"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:40:44.363030+00:00",
"file_format": "fastq",
"file_size": 15889449586,
"href": "/sequence-files/IGVFFI4079XVLD/@@download/IGVFFI4079XVLD.fastq.gz",
"md5sum": "d55924e0965eb5ac6313ceefdf9bb639",
"s3_uri": "s3://igvf-files/2025/03/20/d8f5dcce-b1ec-4db4-9a4e-ca9ba5cecd51/IGVFFI4079XVLD.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_nd_02-27_CBL_X004_S03_L003_B1_T1_P004_S3_L001_R1_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI7279RHVG/",
"accession": "IGVFFI7279RHVG",
"aliases": [
"igvf:corces_sequenceFile_RNA_X004_G3_P004_L001_R2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2025-03-20T00:40:45.550606+00:00",
"file_format": "fastq",
"file_size": 13507729004,
"href": "/sequence-files/IGVFFI7279RHVG/@@download/IGVFFI7279RHVG.fastq.gz",
"md5sum": "f65f69ef2258f2d2094e29bf198cf7ac",
"s3_uri": "s3://igvf-files/2025/03/20/355aefd5-e4b8-4c61-85d2-23d501f68bba/IGVFFI7279RHVG.fastq.gz",
"sequencing_platform": {
"@id": "/platform-terms/EFO_0008637/",
"status": "released",
"term_name": "Illumina NovaSeq 6000"
},
"status": "preview",
"submitted_file_name": "Multiome_RNA_nd_02-27_CBL_X004_S03_L003_B1_T1_P004_S3_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/IGVFFI8751YQRY/"
],
"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/IGVFDS5735HWHA/",
"accession": "IGVFDS5735HWHA",
"status": "preview"
}
],
"samples": [
{
"@id": "/tissues/IGVFSM9133DPZS/",
"@type": [
"Tissue",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9133DPZS",
"aliases": [
"igvf:corces_tissue_BANN0227_CBL_B1"
],
"classifications": [
"tissue"
],
"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_0002129/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "cerebellar cortex",
"term_name": "cerebellar cortex"
}
],
"status": "preview",
"summary": "Homo sapiens (male, 86 years) cerebellar cortex tissue",
"taxa": "Homo sapiens"
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-20T00:40:44.363030+00:00",
"summary": "single-nucleus RNA sequencing assay (10x multiome)",
"uuid": "772c1bdc-9202-470b-9fc3-292fcbf7821f"
}