{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7745YYJB/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7745YYJB",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinB_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS7745YYJB](/measurement-sets/IGVFDS7745YYJB/) has sequence file(s) [IGVFFI2528XYME](/sequence-files/IGVFFI2528XYME/), [IGVFFI6627KJEQ](/sequence-files/IGVFFI6627KJEQ/), [IGVFFI7520EKSE](/sequence-files/IGVFFI7520EKSE/), [IGVFFI0125HUEA](/sequence-files/IGVFFI0125HUEA/), [IGVFFI8618ZKVX](/sequence-files/IGVFFI8618ZKVX/), [IGVFFI5374JPJD](/sequence-files/IGVFFI5374JPJD/), [IGVFFI3405BZVI](/sequence-files/IGVFFI3405BZVI/), [IGVFFI5558AHQU](/sequence-files/IGVFFI5558AHQU/), [IGVFFI8964VFYD](/sequence-files/IGVFFI8964VFYD/), [IGVFFI5325MJIN](/sequence-files/IGVFFI5325MJIN/), [IGVFFI6133RZVA](/sequence-files/IGVFFI6133RZVA/), [IGVFFI0872CNTM](/sequence-files/IGVFFI0872CNTM/), [IGVFFI8791OKXC](/sequence-files/IGVFFI8791OKXC/), [IGVFFI5553QYNW](/sequence-files/IGVFFI5553QYNW/), [IGVFFI1589VNUC](/sequence-files/IGVFFI1589VNUC/), [IGVFFI1746KFEV](/sequence-files/IGVFFI1746KFEV/), [IGVFFI9631ZJXT](/sequence-files/IGVFFI9631ZJXT/), [IGVFFI7444BJTY](/sequence-files/IGVFFI7444BJTY/), [IGVFFI4283XRYV](/sequence-files/IGVFFI4283XRYV/), [IGVFFI4501JDUK](/sequence-files/IGVFFI4501JDUK/), [IGVFFI4079AFQP](/sequence-files/IGVFFI4079AFQP/), [IGVFFI9287DXDV](/sequence-files/IGVFFI9287DXDV/), [IGVFFI2586GBXK](/sequence-files/IGVFFI2586GBXK/), [IGVFFI2785TMQY](/sequence-files/IGVFFI2785TMQY/), [IGVFFI8326NXKH](/sequence-files/IGVFFI8326NXKH/), [IGVFFI7619NIHK](/sequence-files/IGVFFI7619NIHK/), [IGVFFI9004XGMP](/sequence-files/IGVFFI9004XGMP/), [IGVFFI7151SHDG](/sequence-files/IGVFFI7151SHDG/), [IGVFFI8369ZLOO](/sequence-files/IGVFFI8369ZLOO/), [IGVFFI2699MDIT](/sequence-files/IGVFFI2699MDIT/), [IGVFFI6937SYWU](/sequence-files/IGVFFI6937SYWU/), [IGVFFI2965NYEE](/sequence-files/IGVFFI2965NYEE/), [IGVFFI8806XWHY](/sequence-files/IGVFFI8806XWHY/), [IGVFFI1073ZAJL](/sequence-files/IGVFFI1073ZAJL/), [IGVFFI3588HZTG](/sequence-files/IGVFFI3588HZTG/), [IGVFFI7848AYHW](/sequence-files/IGVFFI7848AYHW/), [IGVFFI8971QXUS](/sequence-files/IGVFFI8971QXUS/), [IGVFFI9297KYDW](/sequence-files/IGVFFI9297KYDW/), [IGVFFI0617XXYS](/sequence-files/IGVFFI0617XXYS/), [IGVFFI3822ILRS](/sequence-files/IGVFFI3822ILRS/), [IGVFFI6104OHAI](/sequence-files/IGVFFI6104OHAI/), [IGVFFI3953BYCW](/sequence-files/IGVFFI3953BYCW/), [IGVFFI8613KIEF](/sequence-files/IGVFFI8613KIEF/), [IGVFFI4597JIGZ](/sequence-files/IGVFFI4597JIGZ/), [IGVFFI9829PRVO](/sequence-files/IGVFFI9829PRVO/), [IGVFFI4987TZSS](/sequence-files/IGVFFI4987TZSS/), [IGVFFI4586RVCZ](/sequence-files/IGVFFI4586RVCZ/), [IGVFFI2675GOAU](/sequence-files/IGVFFI2675GOAU/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS7745YYJB/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7745YYJB](/measurement-sets/IGVFDS7745YYJB/) has sequence file(s): [IGVFFI2528XYME](/sequence-files/IGVFFI2528XYME/), [IGVFFI6627KJEQ](/sequence-files/IGVFFI6627KJEQ/), [IGVFFI7520EKSE](/sequence-files/IGVFFI7520EKSE/), [IGVFFI0125HUEA](/sequence-files/IGVFFI0125HUEA/), [IGVFFI8618ZKVX](/sequence-files/IGVFFI8618ZKVX/), [IGVFFI5374JPJD](/sequence-files/IGVFFI5374JPJD/), [IGVFFI3405BZVI](/sequence-files/IGVFFI3405BZVI/), [IGVFFI5558AHQU](/sequence-files/IGVFFI5558AHQU/), [IGVFFI8964VFYD](/sequence-files/IGVFFI8964VFYD/), [IGVFFI5325MJIN](/sequence-files/IGVFFI5325MJIN/), [IGVFFI6133RZVA](/sequence-files/IGVFFI6133RZVA/), [IGVFFI0872CNTM](/sequence-files/IGVFFI0872CNTM/), [IGVFFI8791OKXC](/sequence-files/IGVFFI8791OKXC/), [IGVFFI5553QYNW](/sequence-files/IGVFFI5553QYNW/), [IGVFFI1589VNUC](/sequence-files/IGVFFI1589VNUC/), [IGVFFI1746KFEV](/sequence-files/IGVFFI1746KFEV/), [IGVFFI9631ZJXT](/sequence-files/IGVFFI9631ZJXT/), [IGVFFI7444BJTY](/sequence-files/IGVFFI7444BJTY/), [IGVFFI4283XRYV](/sequence-files/IGVFFI4283XRYV/), [IGVFFI4501JDUK](/sequence-files/IGVFFI4501JDUK/), [IGVFFI4079AFQP](/sequence-files/IGVFFI4079AFQP/), [IGVFFI9287DXDV](/sequence-files/IGVFFI9287DXDV/), [IGVFFI2586GBXK](/sequence-files/IGVFFI2586GBXK/), [IGVFFI2785TMQY](/sequence-files/IGVFFI2785TMQY/), [IGVFFI8326NXKH](/sequence-files/IGVFFI8326NXKH/), [IGVFFI7619NIHK](/sequence-files/IGVFFI7619NIHK/), [IGVFFI9004XGMP](/sequence-files/IGVFFI9004XGMP/), [IGVFFI7151SHDG](/sequence-files/IGVFFI7151SHDG/), [IGVFFI8369ZLOO](/sequence-files/IGVFFI8369ZLOO/), [IGVFFI2699MDIT](/sequence-files/IGVFFI2699MDIT/), [IGVFFI6937SYWU](/sequence-files/IGVFFI6937SYWU/), [IGVFFI2965NYEE](/sequence-files/IGVFFI2965NYEE/), [IGVFFI8806XWHY](/sequence-files/IGVFFI8806XWHY/), [IGVFFI1073ZAJL](/sequence-files/IGVFFI1073ZAJL/), [IGVFFI3588HZTG](/sequence-files/IGVFFI3588HZTG/), [IGVFFI7848AYHW](/sequence-files/IGVFFI7848AYHW/), [IGVFFI8971QXUS](/sequence-files/IGVFFI8971QXUS/), [IGVFFI9297KYDW](/sequence-files/IGVFFI9297KYDW/), [IGVFFI0617XXYS](/sequence-files/IGVFFI0617XXYS/), [IGVFFI3822ILRS](/sequence-files/IGVFFI3822ILRS/), [IGVFFI6104OHAI](/sequence-files/IGVFFI6104OHAI/), [IGVFFI3953BYCW](/sequence-files/IGVFFI3953BYCW/), [IGVFFI8613KIEF](/sequence-files/IGVFFI8613KIEF/), [IGVFFI4597JIGZ](/sequence-files/IGVFFI4597JIGZ/), [IGVFFI9829PRVO](/sequence-files/IGVFFI9829PRVO/), [IGVFFI4987TZSS](/sequence-files/IGVFFI4987TZSS/), [IGVFFI4586RVCZ](/sequence-files/IGVFFI4586RVCZ/), [IGVFFI2675GOAU](/sequence-files/IGVFFI2675GOAU/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS7745YYJB/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7745YYJB](/measurement-sets/IGVFDS7745YYJB/) 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": 40,
"level_name": "WARNING",
"name": "audit_missing_auxiliary_set",
"path": "/measurement-sets/IGVFDS7745YYJB/"
}
]
},
"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"
},
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{
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"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:53:07.937703+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
"file_set_type": "experimental data",
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{
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{
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},
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},
{
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],
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"file_set_type": "guide library",
"status": "preview",
"summary": "guide (sgRNA) library targeting sequence variants in a genomic locus"
}
],
"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
"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": "preview",
"summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
"taxa": "Homo sapiens"
}
],
"schema_version": "23",
"status": "preview",
"submitted_by": {
"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-11-26T06:55:28.096189+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
"targeted_genes": [
{
"@id": "/genes/ENSG00000108179/",
"geneid": "ENSG00000108179",
"name": "peptidylprolyl isomerase F",
"status": "released",
"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": "4d9ec51e-07b0-4fea-9b48-68f25016ba48"
}