{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS0241SXOC/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS0241SXOC",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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 [IGVFDS0241SXOC](/measurement-sets/IGVFDS0241SXOC/) has sequence file(s) [IGVFFI9254NAZS](/sequence-files/IGVFFI9254NAZS/), [IGVFFI9890JVFU](/sequence-files/IGVFFI9890JVFU/), [IGVFFI3923RYGW](/sequence-files/IGVFFI3923RYGW/), [IGVFFI6089QPTL](/sequence-files/IGVFFI6089QPTL/), [IGVFFI5757RANJ](/sequence-files/IGVFFI5757RANJ/), [IGVFFI3314IENP](/sequence-files/IGVFFI3314IENP/), [IGVFFI1003QUAF](/sequence-files/IGVFFI1003QUAF/), [IGVFFI1529XKAC](/sequence-files/IGVFFI1529XKAC/), [IGVFFI5204PUIO](/sequence-files/IGVFFI5204PUIO/), [IGVFFI1820IWRA](/sequence-files/IGVFFI1820IWRA/), [IGVFFI0358DIGX](/sequence-files/IGVFFI0358DIGX/), [IGVFFI8641QGID](/sequence-files/IGVFFI8641QGID/), [IGVFFI2437KQKI](/sequence-files/IGVFFI2437KQKI/), [IGVFFI5470ROKR](/sequence-files/IGVFFI5470ROKR/), [IGVFFI6400ZSMJ](/sequence-files/IGVFFI6400ZSMJ/), [IGVFFI7802WYYB](/sequence-files/IGVFFI7802WYYB/), [IGVFFI0665LMYF](/sequence-files/IGVFFI0665LMYF/), [IGVFFI1971MQPV](/sequence-files/IGVFFI1971MQPV/), [IGVFFI2374RLFO](/sequence-files/IGVFFI2374RLFO/), [IGVFFI8326DMHT](/sequence-files/IGVFFI8326DMHT/), [IGVFFI7922QNFG](/sequence-files/IGVFFI7922QNFG/), [IGVFFI8330EZWJ](/sequence-files/IGVFFI8330EZWJ/), [IGVFFI4066QVOX](/sequence-files/IGVFFI4066QVOX/), [IGVFFI0418SUKX](/sequence-files/IGVFFI0418SUKX/), [IGVFFI1713QMPT](/sequence-files/IGVFFI1713QMPT/), [IGVFFI4879GRBC](/sequence-files/IGVFFI4879GRBC/), [IGVFFI0649SPCS](/sequence-files/IGVFFI0649SPCS/), [IGVFFI2098WIUE](/sequence-files/IGVFFI2098WIUE/), [IGVFFI9541NYER](/sequence-files/IGVFFI9541NYER/), [IGVFFI8964ELTW](/sequence-files/IGVFFI8964ELTW/), [IGVFFI3682HUMT](/sequence-files/IGVFFI3682HUMT/), [IGVFFI3621JPXN](/sequence-files/IGVFFI3621JPXN/), [IGVFFI6249ULSG](/sequence-files/IGVFFI6249ULSG/), [IGVFFI3557HBKT](/sequence-files/IGVFFI3557HBKT/), [IGVFFI3549BCSY](/sequence-files/IGVFFI3549BCSY/), [IGVFFI5148QSBB](/sequence-files/IGVFFI5148QSBB/), [IGVFFI8444DSBK](/sequence-files/IGVFFI8444DSBK/), [IGVFFI1753UYSH](/sequence-files/IGVFFI1753UYSH/), [IGVFFI3067YIJK](/sequence-files/IGVFFI3067YIJK/), [IGVFFI4625YSWG](/sequence-files/IGVFFI4625YSWG/), [IGVFFI9037KHVI](/sequence-files/IGVFFI9037KHVI/), [IGVFFI6791YQEW](/sequence-files/IGVFFI6791YQEW/), [IGVFFI3832DCRN](/sequence-files/IGVFFI3832DCRN/), [IGVFFI0970BEQU](/sequence-files/IGVFFI0970BEQU/), [IGVFFI9255XBFM](/sequence-files/IGVFFI9255XBFM/), [IGVFFI9933UYVQ](/sequence-files/IGVFFI9933UYVQ/), [IGVFFI0033UOVO](/sequence-files/IGVFFI0033UOVO/), [IGVFFI3137APZT](/sequence-files/IGVFFI3137APZT/) 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/IGVFDS0241SXOC/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS0241SXOC](/measurement-sets/IGVFDS0241SXOC/) has sequence file(s): [IGVFFI9254NAZS](/sequence-files/IGVFFI9254NAZS/), [IGVFFI9890JVFU](/sequence-files/IGVFFI9890JVFU/), [IGVFFI3923RYGW](/sequence-files/IGVFFI3923RYGW/), [IGVFFI6089QPTL](/sequence-files/IGVFFI6089QPTL/), [IGVFFI5757RANJ](/sequence-files/IGVFFI5757RANJ/), [IGVFFI3314IENP](/sequence-files/IGVFFI3314IENP/), [IGVFFI1003QUAF](/sequence-files/IGVFFI1003QUAF/), [IGVFFI1529XKAC](/sequence-files/IGVFFI1529XKAC/), [IGVFFI5204PUIO](/sequence-files/IGVFFI5204PUIO/), [IGVFFI1820IWRA](/sequence-files/IGVFFI1820IWRA/), [IGVFFI0358DIGX](/sequence-files/IGVFFI0358DIGX/), [IGVFFI8641QGID](/sequence-files/IGVFFI8641QGID/), [IGVFFI2437KQKI](/sequence-files/IGVFFI2437KQKI/), [IGVFFI5470ROKR](/sequence-files/IGVFFI5470ROKR/), [IGVFFI6400ZSMJ](/sequence-files/IGVFFI6400ZSMJ/), [IGVFFI7802WYYB](/sequence-files/IGVFFI7802WYYB/), [IGVFFI0665LMYF](/sequence-files/IGVFFI0665LMYF/), [IGVFFI1971MQPV](/sequence-files/IGVFFI1971MQPV/), [IGVFFI2374RLFO](/sequence-files/IGVFFI2374RLFO/), [IGVFFI8326DMHT](/sequence-files/IGVFFI8326DMHT/), [IGVFFI7922QNFG](/sequence-files/IGVFFI7922QNFG/), [IGVFFI8330EZWJ](/sequence-files/IGVFFI8330EZWJ/), [IGVFFI4066QVOX](/sequence-files/IGVFFI4066QVOX/), [IGVFFI0418SUKX](/sequence-files/IGVFFI0418SUKX/), [IGVFFI1713QMPT](/sequence-files/IGVFFI1713QMPT/), [IGVFFI4879GRBC](/sequence-files/IGVFFI4879GRBC/), [IGVFFI0649SPCS](/sequence-files/IGVFFI0649SPCS/), [IGVFFI2098WIUE](/sequence-files/IGVFFI2098WIUE/), [IGVFFI9541NYER](/sequence-files/IGVFFI9541NYER/), [IGVFFI8964ELTW](/sequence-files/IGVFFI8964ELTW/), [IGVFFI3682HUMT](/sequence-files/IGVFFI3682HUMT/), [IGVFFI3621JPXN](/sequence-files/IGVFFI3621JPXN/), [IGVFFI6249ULSG](/sequence-files/IGVFFI6249ULSG/), [IGVFFI3557HBKT](/sequence-files/IGVFFI3557HBKT/), [IGVFFI3549BCSY](/sequence-files/IGVFFI3549BCSY/), [IGVFFI5148QSBB](/sequence-files/IGVFFI5148QSBB/), [IGVFFI8444DSBK](/sequence-files/IGVFFI8444DSBK/), [IGVFFI1753UYSH](/sequence-files/IGVFFI1753UYSH/), [IGVFFI3067YIJK](/sequence-files/IGVFFI3067YIJK/), [IGVFFI4625YSWG](/sequence-files/IGVFFI4625YSWG/), [IGVFFI9037KHVI](/sequence-files/IGVFFI9037KHVI/), [IGVFFI6791YQEW](/sequence-files/IGVFFI6791YQEW/), [IGVFFI3832DCRN](/sequence-files/IGVFFI3832DCRN/), [IGVFFI0970BEQU](/sequence-files/IGVFFI0970BEQU/), [IGVFFI9255XBFM](/sequence-files/IGVFFI9255XBFM/), [IGVFFI9933UYVQ](/sequence-files/IGVFFI9933UYVQ/), [IGVFFI0033UOVO](/sequence-files/IGVFFI0033UOVO/), [IGVFFI3137APZT](/sequence-files/IGVFFI3137APZT/) 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/IGVFDS0241SXOC/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS0241SXOC](/measurement-sets/IGVFDS0241SXOC/) 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/IGVFDS0241SXOC/"
}
]
},
"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": "2024-11-25T23:53:54.527033+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO7359LVPI/",
"accession": "IGVFDO7359LVPI",
"aliases": [
"igvf:donor_of_THP1"
],
"sex": "male",
"status": "released",
"taxa": "Homo sapiens"
}
],
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"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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"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 51-75% 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": "2024-11-26T07:26:01.299976+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": "e65ef96c-6bf3-4b0c-8cf6-507cdaffed80"
}