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{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7886YBBF](/measurement-sets/IGVFDS7886YBBF/) has sequence file(s): [IGVFFI2570YFTN](/sequence-files/IGVFFI2570YFTN/), [IGVFFI9458VKIC](/sequence-files/IGVFFI9458VKIC/), [IGVFFI3223SWOX](/sequence-files/IGVFFI3223SWOX/), [IGVFFI9797PDEM](/sequence-files/IGVFFI9797PDEM/), [IGVFFI0311KWLV](/sequence-files/IGVFFI0311KWLV/), [IGVFFI0824WVUR](/sequence-files/IGVFFI0824WVUR/), [IGVFFI2899URUY](/sequence-files/IGVFFI2899URUY/), [IGVFFI2048WLMS](/sequence-files/IGVFFI2048WLMS/), [IGVFFI5973JRPW](/sequence-files/IGVFFI5973JRPW/), [IGVFFI7758HWUP](/sequence-files/IGVFFI7758HWUP/), [IGVFFI2124BYKV](/sequence-files/IGVFFI2124BYKV/), [IGVFFI2315KVZJ](/sequence-files/IGVFFI2315KVZJ/) 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/IGVFDS7886YBBF/"
},
{
"category": "missing strand specificity",
"detail": "Measurement set [IGVFDS7886YBBF](/measurement-sets/IGVFDS7886YBBF/) 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/IGVFDS7886YBBF/"
}
],
"WARNING": [
{
"category": "missing analysis",
"detail": "Measurement set [IGVFDS7886YBBF](/measurement-sets/IGVFDS7886YBBF/) 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/IGVFDS7886YBBF/"
}
]
},
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"contact_pi": {
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"title": "Ansuman Satpathy"
},
"title": "Single-cell Mapping Center for Human Regulatory Elements and Gene Activity"
},
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"controlled_access": false,
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"data_use_limitation_summaries": [
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],
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],
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},
{
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"igvf:corces_donor_BANN0325"
],
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},
{
"@id": "/human-donors/IGVFDO2028IGVN/",
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"igvf:corces_donor_BANN1256"
],
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},
{
"@id": "/human-donors/IGVFDO1464XWYC/",
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"igvf:corces_donor_BANN1809"
],
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},
{
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"igvf:corces_donor_BANN1554"
],
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},
{
"@id": "/human-donors/IGVFDO3971UIZC/",
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],
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},
{
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],
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},
{
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],
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}
],
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},
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},
{
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],
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},
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},
{
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},
{
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},
{
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},
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},
{
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{
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{
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{
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},
{
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],
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},
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}
],
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"lab": {
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"title": "Ryan Corces, Gladstone Institute UCSF"
},
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"onlist_files": [
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],
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"protocols": [
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],
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{
"@id": "/measurement-sets/IGVFDS9901CQZL/",
"accession": "IGVFDS9901CQZL",
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}
],
"samples": [
{
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"@type": [
"MultiplexedSample",
"Sample",
"Item"
],
"accession": "IGVFSM9620UKJQ",
"aliases": [
"igvf:corces_multiplexedSample_RP033_G6"
],
"classifications": [
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"multiplexed sample"
],
"disease_terms": [
{
"@id": "/phenotype-terms/DOID_14330/",
"status": "in progress",
"term_name": "Parkinson's disease"
},
{
"@id": "/phenotype-terms/DOID_9246/",
"status": "in progress",
"term_name": "cerebral amyloid angiopathy"
}
],
"institutional_certificates": [
{
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"certificate_identifier": "IP115-05",
"controlled_access": false,
"status": "in progress"
}
],
"modifications": [],
"sample_terms": [
{
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"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "putamen",
"term_name": "putamen"
},
{
"@id": "/sample-terms/UBERON_0002038/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "substantia nigra",
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},
{
"@id": "/sample-terms/UBERON_0002740/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"status": "preview",
"summary": "posterior cingulate gyrus",
"term_name": "posterior cingulate gyrus"
}
],
"status": "preview",
"summary": "multiplexed sample: Homo sapiens (male, 70 years) substantia nigra tissue associated with Parkinson's disease; Homo sapiens (female, 70 years) substantia nigra tissue associated with Parkinson's disease; ... and 6 more samples",
"taxa": "Homo sapiens",
"treatments": []
}
],
"schema_version": "26",
"status": "preview",
"submitted_by": {
"@id": "/users/c13db3ca-f844-4a69-9056-5fbc4a100f36/",
"title": "Ryan Corces"
},
"submitted_files_timestamp": "2025-03-21T04:02:02.571830+00:00",
"summary": "single-nucleus ATAC-seq (10x multiome)",
"uuid": "e5c6199b-b45c-4a87-b036-fdb00cb9ef29"
}