{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS4607VBYI/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS4607VBYI",
"aliases": [
"jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinC_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 [IGVFDS4607VBYI](/measurement-sets/IGVFDS4607VBYI/) has sequence file(s) [IGVFFI8535WPRB](/sequence-files/IGVFFI8535WPRB/), [IGVFFI1915WRNJ](/sequence-files/IGVFFI1915WRNJ/), [IGVFFI3409DOPF](/sequence-files/IGVFFI3409DOPF/), [IGVFFI9975VMPG](/sequence-files/IGVFFI9975VMPG/), [IGVFFI2547ZAPS](/sequence-files/IGVFFI2547ZAPS/), [IGVFFI8823PPPH](/sequence-files/IGVFFI8823PPPH/), [IGVFFI5255XVXG](/sequence-files/IGVFFI5255XVXG/), [IGVFFI9879PLDL](/sequence-files/IGVFFI9879PLDL/), [IGVFFI9892AUNZ](/sequence-files/IGVFFI9892AUNZ/), [IGVFFI9583EGLM](/sequence-files/IGVFFI9583EGLM/), [IGVFFI9116KCZE](/sequence-files/IGVFFI9116KCZE/), [IGVFFI6218OIZZ](/sequence-files/IGVFFI6218OIZZ/), [IGVFFI1789VKOW](/sequence-files/IGVFFI1789VKOW/), [IGVFFI3851EEZQ](/sequence-files/IGVFFI3851EEZQ/), [IGVFFI1066SCXZ](/sequence-files/IGVFFI1066SCXZ/), [IGVFFI5178OSMB](/sequence-files/IGVFFI5178OSMB/), [IGVFFI2042OSKG](/sequence-files/IGVFFI2042OSKG/), [IGVFFI8091NCVM](/sequence-files/IGVFFI8091NCVM/), [IGVFFI4268NQVA](/sequence-files/IGVFFI4268NQVA/), [IGVFFI9976KWSL](/sequence-files/IGVFFI9976KWSL/), [IGVFFI7424WHZL](/sequence-files/IGVFFI7424WHZL/), [IGVFFI0901FCDI](/sequence-files/IGVFFI0901FCDI/), [IGVFFI5501FBZH](/sequence-files/IGVFFI5501FBZH/), [IGVFFI6344VMDE](/sequence-files/IGVFFI6344VMDE/), [IGVFFI6631HHMI](/sequence-files/IGVFFI6631HHMI/), [IGVFFI3033HJEC](/sequence-files/IGVFFI3033HJEC/), [IGVFFI9848XAKV](/sequence-files/IGVFFI9848XAKV/), [IGVFFI8636AQPQ](/sequence-files/IGVFFI8636AQPQ/), [IGVFFI2159CKRH](/sequence-files/IGVFFI2159CKRH/), [IGVFFI9278YZLM](/sequence-files/IGVFFI9278YZLM/), [IGVFFI8940MBEW](/sequence-files/IGVFFI8940MBEW/), [IGVFFI8759ETWA](/sequence-files/IGVFFI8759ETWA/), [IGVFFI3271DFPJ](/sequence-files/IGVFFI3271DFPJ/), [IGVFFI5499NUFW](/sequence-files/IGVFFI5499NUFW/), [IGVFFI8638SCPF](/sequence-files/IGVFFI8638SCPF/), [IGVFFI3351KGBJ](/sequence-files/IGVFFI3351KGBJ/), [IGVFFI2771BIBC](/sequence-files/IGVFFI2771BIBC/), [IGVFFI8702LPQC](/sequence-files/IGVFFI8702LPQC/), [IGVFFI7165WPIE](/sequence-files/IGVFFI7165WPIE/), [IGVFFI6598RJQD](/sequence-files/IGVFFI6598RJQD/), [IGVFFI7563ICEU](/sequence-files/IGVFFI7563ICEU/), [IGVFFI9851CITF](/sequence-files/IGVFFI9851CITF/), [IGVFFI4940XPEA](/sequence-files/IGVFFI4940XPEA/), [IGVFFI3407NDDY](/sequence-files/IGVFFI3407NDDY/), [IGVFFI9711TOSB](/sequence-files/IGVFFI9711TOSB/), [IGVFFI7762BNDF](/sequence-files/IGVFFI7762BNDF/), [IGVFFI5782OJBQ](/sequence-files/IGVFFI5782OJBQ/), [IGVFFI4100DNIV](/sequence-files/IGVFFI4100DNIV/) 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/IGVFDS4607VBYI/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS4607VBYI](/measurement-sets/IGVFDS4607VBYI/) has sequence file(s): [IGVFFI8535WPRB](/sequence-files/IGVFFI8535WPRB/), [IGVFFI1915WRNJ](/sequence-files/IGVFFI1915WRNJ/), [IGVFFI3409DOPF](/sequence-files/IGVFFI3409DOPF/), [IGVFFI9975VMPG](/sequence-files/IGVFFI9975VMPG/), [IGVFFI2547ZAPS](/sequence-files/IGVFFI2547ZAPS/), [IGVFFI8823PPPH](/sequence-files/IGVFFI8823PPPH/), [IGVFFI5255XVXG](/sequence-files/IGVFFI5255XVXG/), [IGVFFI9879PLDL](/sequence-files/IGVFFI9879PLDL/), [IGVFFI9892AUNZ](/sequence-files/IGVFFI9892AUNZ/), [IGVFFI9583EGLM](/sequence-files/IGVFFI9583EGLM/), [IGVFFI9116KCZE](/sequence-files/IGVFFI9116KCZE/), [IGVFFI6218OIZZ](/sequence-files/IGVFFI6218OIZZ/), [IGVFFI1789VKOW](/sequence-files/IGVFFI1789VKOW/), [IGVFFI3851EEZQ](/sequence-files/IGVFFI3851EEZQ/), [IGVFFI1066SCXZ](/sequence-files/IGVFFI1066SCXZ/), [IGVFFI5178OSMB](/sequence-files/IGVFFI5178OSMB/), [IGVFFI2042OSKG](/sequence-files/IGVFFI2042OSKG/), [IGVFFI8091NCVM](/sequence-files/IGVFFI8091NCVM/), [IGVFFI4268NQVA](/sequence-files/IGVFFI4268NQVA/), [IGVFFI9976KWSL](/sequence-files/IGVFFI9976KWSL/), [IGVFFI7424WHZL](/sequence-files/IGVFFI7424WHZL/), [IGVFFI0901FCDI](/sequence-files/IGVFFI0901FCDI/), [IGVFFI5501FBZH](/sequence-files/IGVFFI5501FBZH/), [IGVFFI6344VMDE](/sequence-files/IGVFFI6344VMDE/), [IGVFFI6631HHMI](/sequence-files/IGVFFI6631HHMI/), [IGVFFI3033HJEC](/sequence-files/IGVFFI3033HJEC/), [IGVFFI9848XAKV](/sequence-files/IGVFFI9848XAKV/), [IGVFFI8636AQPQ](/sequence-files/IGVFFI8636AQPQ/), [IGVFFI2159CKRH](/sequence-files/IGVFFI2159CKRH/), [IGVFFI9278YZLM](/sequence-files/IGVFFI9278YZLM/), [IGVFFI8940MBEW](/sequence-files/IGVFFI8940MBEW/), [IGVFFI8759ETWA](/sequence-files/IGVFFI8759ETWA/), [IGVFFI3271DFPJ](/sequence-files/IGVFFI3271DFPJ/), [IGVFFI5499NUFW](/sequence-files/IGVFFI5499NUFW/), [IGVFFI8638SCPF](/sequence-files/IGVFFI8638SCPF/), [IGVFFI3351KGBJ](/sequence-files/IGVFFI3351KGBJ/), [IGVFFI2771BIBC](/sequence-files/IGVFFI2771BIBC/), [IGVFFI8702LPQC](/sequence-files/IGVFFI8702LPQC/), [IGVFFI7165WPIE](/sequence-files/IGVFFI7165WPIE/), [IGVFFI6598RJQD](/sequence-files/IGVFFI6598RJQD/), [IGVFFI7563ICEU](/sequence-files/IGVFFI7563ICEU/), [IGVFFI9851CITF](/sequence-files/IGVFFI9851CITF/), [IGVFFI4940XPEA](/sequence-files/IGVFFI4940XPEA/), [IGVFFI3407NDDY](/sequence-files/IGVFFI3407NDDY/), [IGVFFI9711TOSB](/sequence-files/IGVFFI9711TOSB/), [IGVFFI7762BNDF](/sequence-files/IGVFFI7762BNDF/), [IGVFFI5782OJBQ](/sequence-files/IGVFFI5782OJBQ/), [IGVFFI4100DNIV](/sequence-files/IGVFFI4100DNIV/) 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/IGVFDS4607VBYI/"
},
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM8654CBKP](/in-vitro-systems/IGVFSM8654CBKP/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM8654CBKP/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS4607VBYI](/measurement-sets/IGVFDS4607VBYI/) 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/IGVFDS4607VBYI/"
}
]
},
"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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],
"status": "released"
}
],
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"creation_timestamp": "2023-12-13T08:01:39.009563+00:00",
"donors": [
{
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"accession": "IGVFDO7359LVPI",
"aliases": [
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],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
"externally_hosted": false,
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},
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"@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2023-12-13T08:25:32.055548+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": "b75addc9-5b0d-4bea-adb8-9476f29c7ecb"
}