{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7816HTLM/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7816HTLM",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinA_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 [IGVFDS7816HTLM](/measurement-sets/IGVFDS7816HTLM/) has sequence file(s) [IGVFFI5942IANF](/sequence-files/IGVFFI5942IANF/), [IGVFFI5923ETNG](/sequence-files/IGVFFI5923ETNG/), [IGVFFI1213QMFJ](/sequence-files/IGVFFI1213QMFJ/), [IGVFFI1584EDNH](/sequence-files/IGVFFI1584EDNH/), [IGVFFI1964BGXX](/sequence-files/IGVFFI1964BGXX/), [IGVFFI7038HAGL](/sequence-files/IGVFFI7038HAGL/), [IGVFFI2183CMSE](/sequence-files/IGVFFI2183CMSE/), [IGVFFI6505HGXG](/sequence-files/IGVFFI6505HGXG/), [IGVFFI9966EEPM](/sequence-files/IGVFFI9966EEPM/), [IGVFFI4013LQXL](/sequence-files/IGVFFI4013LQXL/), [IGVFFI0698AAZB](/sequence-files/IGVFFI0698AAZB/), [IGVFFI1128IOXL](/sequence-files/IGVFFI1128IOXL/), [IGVFFI7781YNPV](/sequence-files/IGVFFI7781YNPV/), [IGVFFI9497SENF](/sequence-files/IGVFFI9497SENF/), [IGVFFI3175DBHP](/sequence-files/IGVFFI3175DBHP/), [IGVFFI3184EIDL](/sequence-files/IGVFFI3184EIDL/), [IGVFFI3413EEIK](/sequence-files/IGVFFI3413EEIK/), [IGVFFI8940RGZD](/sequence-files/IGVFFI8940RGZD/), [IGVFFI5412APWD](/sequence-files/IGVFFI5412APWD/), [IGVFFI3348BXFG](/sequence-files/IGVFFI3348BXFG/), [IGVFFI3651EAGP](/sequence-files/IGVFFI3651EAGP/), [IGVFFI6292INPX](/sequence-files/IGVFFI6292INPX/), [IGVFFI1067TNGS](/sequence-files/IGVFFI1067TNGS/), [IGVFFI3253GUJX](/sequence-files/IGVFFI3253GUJX/), [IGVFFI8264LDVT](/sequence-files/IGVFFI8264LDVT/), [IGVFFI9658ALFK](/sequence-files/IGVFFI9658ALFK/), [IGVFFI0888NHLN](/sequence-files/IGVFFI0888NHLN/), [IGVFFI9955SBSK](/sequence-files/IGVFFI9955SBSK/), [IGVFFI8983ONAQ](/sequence-files/IGVFFI8983ONAQ/), [IGVFFI9920BUIU](/sequence-files/IGVFFI9920BUIU/), [IGVFFI4538ZPGK](/sequence-files/IGVFFI4538ZPGK/), [IGVFFI4234VCPX](/sequence-files/IGVFFI4234VCPX/), [IGVFFI8576CXDA](/sequence-files/IGVFFI8576CXDA/), [IGVFFI8090CPRR](/sequence-files/IGVFFI8090CPRR/), [IGVFFI1585HKQD](/sequence-files/IGVFFI1585HKQD/), [IGVFFI4599GKNV](/sequence-files/IGVFFI4599GKNV/), [IGVFFI4284HORS](/sequence-files/IGVFFI4284HORS/), [IGVFFI8889DQDM](/sequence-files/IGVFFI8889DQDM/), [IGVFFI6183LVPZ](/sequence-files/IGVFFI6183LVPZ/), [IGVFFI4384EKYV](/sequence-files/IGVFFI4384EKYV/), [IGVFFI6082WOZU](/sequence-files/IGVFFI6082WOZU/), [IGVFFI8829JTHU](/sequence-files/IGVFFI8829JTHU/), [IGVFFI1396RWWW](/sequence-files/IGVFFI1396RWWW/), [IGVFFI2861QISP](/sequence-files/IGVFFI2861QISP/), [IGVFFI4238LQCR](/sequence-files/IGVFFI4238LQCR/), [IGVFFI2652GBLV](/sequence-files/IGVFFI2652GBLV/), [IGVFFI4020KNUW](/sequence-files/IGVFFI4020KNUW/), [IGVFFI3416BDZQ](/sequence-files/IGVFFI3416BDZQ/) 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/IGVFDS7816HTLM/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7816HTLM](/measurement-sets/IGVFDS7816HTLM/) has sequence file(s): [IGVFFI5942IANF](/sequence-files/IGVFFI5942IANF/), [IGVFFI5923ETNG](/sequence-files/IGVFFI5923ETNG/), [IGVFFI1213QMFJ](/sequence-files/IGVFFI1213QMFJ/), [IGVFFI1584EDNH](/sequence-files/IGVFFI1584EDNH/), [IGVFFI1964BGXX](/sequence-files/IGVFFI1964BGXX/), [IGVFFI7038HAGL](/sequence-files/IGVFFI7038HAGL/), [IGVFFI2183CMSE](/sequence-files/IGVFFI2183CMSE/), [IGVFFI6505HGXG](/sequence-files/IGVFFI6505HGXG/), [IGVFFI9966EEPM](/sequence-files/IGVFFI9966EEPM/), [IGVFFI4013LQXL](/sequence-files/IGVFFI4013LQXL/), [IGVFFI0698AAZB](/sequence-files/IGVFFI0698AAZB/), [IGVFFI1128IOXL](/sequence-files/IGVFFI1128IOXL/), [IGVFFI7781YNPV](/sequence-files/IGVFFI7781YNPV/), [IGVFFI9497SENF](/sequence-files/IGVFFI9497SENF/), [IGVFFI3175DBHP](/sequence-files/IGVFFI3175DBHP/), [IGVFFI3184EIDL](/sequence-files/IGVFFI3184EIDL/), [IGVFFI3413EEIK](/sequence-files/IGVFFI3413EEIK/), [IGVFFI8940RGZD](/sequence-files/IGVFFI8940RGZD/), [IGVFFI5412APWD](/sequence-files/IGVFFI5412APWD/), [IGVFFI3348BXFG](/sequence-files/IGVFFI3348BXFG/), [IGVFFI3651EAGP](/sequence-files/IGVFFI3651EAGP/), [IGVFFI6292INPX](/sequence-files/IGVFFI6292INPX/), [IGVFFI1067TNGS](/sequence-files/IGVFFI1067TNGS/), [IGVFFI3253GUJX](/sequence-files/IGVFFI3253GUJX/), [IGVFFI8264LDVT](/sequence-files/IGVFFI8264LDVT/), [IGVFFI9658ALFK](/sequence-files/IGVFFI9658ALFK/), [IGVFFI0888NHLN](/sequence-files/IGVFFI0888NHLN/), [IGVFFI9955SBSK](/sequence-files/IGVFFI9955SBSK/), [IGVFFI8983ONAQ](/sequence-files/IGVFFI8983ONAQ/), [IGVFFI9920BUIU](/sequence-files/IGVFFI9920BUIU/), [IGVFFI4538ZPGK](/sequence-files/IGVFFI4538ZPGK/), [IGVFFI4234VCPX](/sequence-files/IGVFFI4234VCPX/), [IGVFFI8576CXDA](/sequence-files/IGVFFI8576CXDA/), [IGVFFI8090CPRR](/sequence-files/IGVFFI8090CPRR/), [IGVFFI1585HKQD](/sequence-files/IGVFFI1585HKQD/), [IGVFFI4599GKNV](/sequence-files/IGVFFI4599GKNV/), [IGVFFI4284HORS](/sequence-files/IGVFFI4284HORS/), [IGVFFI8889DQDM](/sequence-files/IGVFFI8889DQDM/), [IGVFFI6183LVPZ](/sequence-files/IGVFFI6183LVPZ/), [IGVFFI4384EKYV](/sequence-files/IGVFFI4384EKYV/), [IGVFFI6082WOZU](/sequence-files/IGVFFI6082WOZU/), [IGVFFI8829JTHU](/sequence-files/IGVFFI8829JTHU/), [IGVFFI1396RWWW](/sequence-files/IGVFFI1396RWWW/), [IGVFFI2861QISP](/sequence-files/IGVFFI2861QISP/), [IGVFFI4238LQCR](/sequence-files/IGVFFI4238LQCR/), [IGVFFI2652GBLV](/sequence-files/IGVFFI2652GBLV/), [IGVFFI4020KNUW](/sequence-files/IGVFFI4020KNUW/), [IGVFFI3416BDZQ](/sequence-files/IGVFFI3416BDZQ/) 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/IGVFDS7816HTLM/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7816HTLM](/measurement-sets/IGVFDS7816HTLM/) 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/IGVFDS7816HTLM/"
}
]
},
"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": "2024-11-25T23:54:07.604289+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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"@id": "/construct-library-sets/IGVFDS4955GEYO/",
"accession": "IGVFDS4955GEYO",
"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 0-25% 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": "2024-11-26T07:41:00.600616+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": "2f8878d8-a47d-4119-b22b-84fa611c68c7"
}