{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS9084GQXI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS9084GQXI",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released measurement set [IGVFDS9084GQXI](/measurement-sets/IGVFDS9084GQXI/) has in progress subobject auxiliary set [IGVFDS8670CGJN](/auxiliary-sets/IGVFDS8670CGJN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/measurement-sets/IGVFDS9084GQXI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM9197BHPY](/in-vitro-systems/IGVFSM9197BHPY/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM9197BHPY/"
}
],
"NOT_COMPLIANT": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS9084GQXI](/measurement-sets/IGVFDS9084GQXI/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS9084GQXI/"
},
{
"category": "missing sequence specification",
"detail": "Auxiliary set [IGVFDS8670CGJN](/auxiliary-sets/IGVFDS8670CGJN/) has sequence file(s): [IGVFFI3493LQYH](/sequence-files/IGVFFI3493LQYH/), [IGVFFI1020CWLC](/sequence-files/IGVFFI1020CWLC/), [IGVFFI2874EVOC](/sequence-files/IGVFFI2874EVOC/), [IGVFFI5138TEHH](/sequence-files/IGVFFI5138TEHH/), [IGVFFI6144OTDA](/sequence-files/IGVFFI6144OTDA/), [IGVFFI6023IKOG](/sequence-files/IGVFFI6023IKOG/), [IGVFFI0618ASUQ](/sequence-files/IGVFFI0618ASUQ/), [IGVFFI2690PYKK](/sequence-files/IGVFFI2690PYKK/), [IGVFFI5657IMCR](/sequence-files/IGVFFI5657IMCR/), [IGVFFI6197NIBR](/sequence-files/IGVFFI6197NIBR/), [IGVFFI1987HYED](/sequence-files/IGVFFI1987HYED/), [IGVFFI4548ESWJ](/sequence-files/IGVFFI4548ESWJ/), [IGVFFI7885ZIVB](/sequence-files/IGVFFI7885ZIVB/), [IGVFFI4282VMAQ](/sequence-files/IGVFFI4282VMAQ/), [IGVFFI3979DDMK](/sequence-files/IGVFFI3979DDMK/), [IGVFFI0931NQDG](/sequence-files/IGVFFI0931NQDG/), [IGVFFI9687BRHO](/sequence-files/IGVFFI9687BRHO/), [IGVFFI2060ROTQ](/sequence-files/IGVFFI2060ROTQ/), [IGVFFI1868UTYC](/sequence-files/IGVFFI1868UTYC/), [IGVFFI1481PBOV](/sequence-files/IGVFFI1481PBOV/), [IGVFFI4450ZWLZ](/sequence-files/IGVFFI4450ZWLZ/), [IGVFFI5366RURL](/sequence-files/IGVFFI5366RURL/), [IGVFFI0599BVTT](/sequence-files/IGVFFI0599BVTT/), [IGVFFI2830RDUV](/sequence-files/IGVFFI2830RDUV/), [IGVFFI8382QQHA](/sequence-files/IGVFFI8382QQHA/), [IGVFFI8563ZXSP](/sequence-files/IGVFFI8563ZXSP/), [IGVFFI6515FHQJ](/sequence-files/IGVFFI6515FHQJ/), [IGVFFI0105YZSM](/sequence-files/IGVFFI0105YZSM/), [IGVFFI6121RRLU](/sequence-files/IGVFFI6121RRLU/), [IGVFFI5329MTKF](/sequence-files/IGVFFI5329MTKF/), [IGVFFI0488NDBE](/sequence-files/IGVFFI0488NDBE/), [IGVFFI2095ERFT](/sequence-files/IGVFFI2095ERFT/), [IGVFFI7912FERB](/sequence-files/IGVFFI7912FERB/), [IGVFFI0812OLJX](/sequence-files/IGVFFI0812OLJX/), [IGVFFI5709QJRK](/sequence-files/IGVFFI5709QJRK/), [IGVFFI7704YFVA](/sequence-files/IGVFFI7704YFVA/), [IGVFFI3424LOUZ](/sequence-files/IGVFFI3424LOUZ/), [IGVFFI6996GIPN](/sequence-files/IGVFFI6996GIPN/), [IGVFFI9277WRZZ](/sequence-files/IGVFFI9277WRZZ/), [IGVFFI1340WNTY](/sequence-files/IGVFFI1340WNTY/), [IGVFFI2459OHKV](/sequence-files/IGVFFI2459OHKV/), [IGVFFI7356USMV](/sequence-files/IGVFFI7356USMV/), [IGVFFI1495EEGA](/sequence-files/IGVFFI1495EEGA/), [IGVFFI3479ZTAU](/sequence-files/IGVFFI3479ZTAU/), [IGVFFI2110EZDX](/sequence-files/IGVFFI2110EZDX/), [IGVFFI5314RTLP](/sequence-files/IGVFFI5314RTLP/), [IGVFFI9135WKOU](/sequence-files/IGVFFI9135WKOU/), [IGVFFI0410ZOZN](/sequence-files/IGVFFI0410ZOZN/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 50,
"level_name": "NOT_COMPLIANT",
"name": "audit_missing_seqspec",
"path": "/auxiliary-sets/IGVFDS8670CGJN/"
}
],
"WARNING": [
{
"category": "missing sequencing kit",
"detail": "Auxiliary set [IGVFDS8670CGJN](/auxiliary-sets/IGVFDS8670CGJN/) has sequence file(s) [IGVFFI3493LQYH](/sequence-files/IGVFFI3493LQYH/), [IGVFFI1020CWLC](/sequence-files/IGVFFI1020CWLC/), [IGVFFI2874EVOC](/sequence-files/IGVFFI2874EVOC/), [IGVFFI5138TEHH](/sequence-files/IGVFFI5138TEHH/), [IGVFFI6144OTDA](/sequence-files/IGVFFI6144OTDA/), [IGVFFI6023IKOG](/sequence-files/IGVFFI6023IKOG/), [IGVFFI0618ASUQ](/sequence-files/IGVFFI0618ASUQ/), [IGVFFI2690PYKK](/sequence-files/IGVFFI2690PYKK/), [IGVFFI5657IMCR](/sequence-files/IGVFFI5657IMCR/), [IGVFFI6197NIBR](/sequence-files/IGVFFI6197NIBR/), [IGVFFI1987HYED](/sequence-files/IGVFFI1987HYED/), [IGVFFI4548ESWJ](/sequence-files/IGVFFI4548ESWJ/), [IGVFFI7885ZIVB](/sequence-files/IGVFFI7885ZIVB/), [IGVFFI4282VMAQ](/sequence-files/IGVFFI4282VMAQ/), [IGVFFI3979DDMK](/sequence-files/IGVFFI3979DDMK/), [IGVFFI0931NQDG](/sequence-files/IGVFFI0931NQDG/), [IGVFFI9687BRHO](/sequence-files/IGVFFI9687BRHO/), [IGVFFI2060ROTQ](/sequence-files/IGVFFI2060ROTQ/), [IGVFFI1868UTYC](/sequence-files/IGVFFI1868UTYC/), [IGVFFI1481PBOV](/sequence-files/IGVFFI1481PBOV/), [IGVFFI4450ZWLZ](/sequence-files/IGVFFI4450ZWLZ/), [IGVFFI5366RURL](/sequence-files/IGVFFI5366RURL/), [IGVFFI0599BVTT](/sequence-files/IGVFFI0599BVTT/), [IGVFFI2830RDUV](/sequence-files/IGVFFI2830RDUV/), [IGVFFI8382QQHA](/sequence-files/IGVFFI8382QQHA/), [IGVFFI8563ZXSP](/sequence-files/IGVFFI8563ZXSP/), [IGVFFI6515FHQJ](/sequence-files/IGVFFI6515FHQJ/), [IGVFFI0105YZSM](/sequence-files/IGVFFI0105YZSM/), [IGVFFI6121RRLU](/sequence-files/IGVFFI6121RRLU/), [IGVFFI5329MTKF](/sequence-files/IGVFFI5329MTKF/), [IGVFFI0488NDBE](/sequence-files/IGVFFI0488NDBE/), [IGVFFI2095ERFT](/sequence-files/IGVFFI2095ERFT/), [IGVFFI7912FERB](/sequence-files/IGVFFI7912FERB/), [IGVFFI0812OLJX](/sequence-files/IGVFFI0812OLJX/), [IGVFFI5709QJRK](/sequence-files/IGVFFI5709QJRK/), [IGVFFI7704YFVA](/sequence-files/IGVFFI7704YFVA/), [IGVFFI3424LOUZ](/sequence-files/IGVFFI3424LOUZ/), [IGVFFI6996GIPN](/sequence-files/IGVFFI6996GIPN/), [IGVFFI9277WRZZ](/sequence-files/IGVFFI9277WRZZ/), [IGVFFI1340WNTY](/sequence-files/IGVFFI1340WNTY/), [IGVFFI2459OHKV](/sequence-files/IGVFFI2459OHKV/), [IGVFFI7356USMV](/sequence-files/IGVFFI7356USMV/), [IGVFFI1495EEGA](/sequence-files/IGVFFI1495EEGA/), [IGVFFI3479ZTAU](/sequence-files/IGVFFI3479ZTAU/), [IGVFFI2110EZDX](/sequence-files/IGVFFI2110EZDX/), [IGVFFI5314RTLP](/sequence-files/IGVFFI5314RTLP/), [IGVFFI9135WKOU](/sequence-files/IGVFFI9135WKOU/), [IGVFFI0410ZOZN](/sequence-files/IGVFFI0410ZOZN/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 40,
"level_name": "WARNING",
"name": "audit_inconsistent_sequencing_kit",
"path": "/auxiliary-sets/IGVFDS8670CGJN/"
},
{
"category": "missing analysis",
"detail": "Auxiliary set [IGVFDS8670CGJN](/auxiliary-sets/IGVFDS8670CGJN/) 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_file_set_for",
"path": "/auxiliary-sets/IGVFDS8670CGJN/"
}
]
},
"auxiliary_sets": [
{
"@id": "/auxiliary-sets/IGVFDS8670CGJN/",
"accession": "IGVFDS8670CGJN",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing_AuxiliarySet"
],
"file_set_type": "variant sequencing"
}
],
"award": {
"@id": "/awards/HG011972/",
"component": "functional characterization",
"contact_pi": {
"@id": "/users/6c75dbfa-635e-4a7a-8ec8-9e51e9c380a4/",
"title": "Jesse Engreitz"
},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
"control_file_sets": [
{
"@id": "/measurement-sets/IGVFDS5864UGFT/",
"accession": "IGVFDS5864UGFT",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
]
}
],
"control_for": [],
"creation_timestamp": "2023-11-30T22:49:40.149812+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"file_set_type": "experimental data",
"files": [],
"input_file_set_for": [
"/analysis-sets/IGVFDS3423PSID/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
"preferred_assay_title": "Variant FlowFISH",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"release_timestamp": "2023-12-20T23:06:39.923270+00:00",
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9197BHPY/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9197BHPY",
"aliases": [
"jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep2-BinD"
],
"classifications": [
"cell line"
],
"construct_library_sets": [
{
"@id": "/construct-library-sets/IGVFDS6982DESN/",
"accession": "IGVFDS6982DESN",
"file_set_type": "guide library",
"summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing"
}
],
"sample_terms": [
{
"@id": "/sample-terms/EFO_0001253/",
"@type": [
"SampleTerm",
"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "released",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% expression of PPIF) modified with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "21",
"status": "released",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-05T20:22:20.523970+00:00",
"summary": "Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"symbol": "PPIF",
"synonyms": [
"rotamase F",
"CYP3",
"cyclophilin F",
"mitochondrial cyclophilin",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"CypD",
"Cyp-D",
"cyclophilin 3",
"cyclophilin D",
"CyP-M",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIase F"
]
}
],
"uuid": "4bff112f-fce1-46c5-82b5-9e07724f345f"
}