{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS2695EXAH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS2695EXAH",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep1-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 [IGVFDS2695EXAH](/measurement-sets/IGVFDS2695EXAH/) has sequence file(s) [IGVFFI1756GREJ](/sequence-files/IGVFFI1756GREJ/), [IGVFFI8519TQWA](/sequence-files/IGVFFI8519TQWA/), [IGVFFI9792PHWJ](/sequence-files/IGVFFI9792PHWJ/), [IGVFFI2931SVNR](/sequence-files/IGVFFI2931SVNR/), [IGVFFI1987HBUL](/sequence-files/IGVFFI1987HBUL/), [IGVFFI8399XWTB](/sequence-files/IGVFFI8399XWTB/), [IGVFFI5400CCTJ](/sequence-files/IGVFFI5400CCTJ/), [IGVFFI2420YPWP](/sequence-files/IGVFFI2420YPWP/), [IGVFFI8348CLAQ](/sequence-files/IGVFFI8348CLAQ/), [IGVFFI7433GVOV](/sequence-files/IGVFFI7433GVOV/), [IGVFFI9903DLEC](/sequence-files/IGVFFI9903DLEC/), [IGVFFI8636AMQF](/sequence-files/IGVFFI8636AMQF/), [IGVFFI9086XFBF](/sequence-files/IGVFFI9086XFBF/), [IGVFFI3905WDCB](/sequence-files/IGVFFI3905WDCB/), [IGVFFI4355UMXI](/sequence-files/IGVFFI4355UMXI/), [IGVFFI3438NHNW](/sequence-files/IGVFFI3438NHNW/), [IGVFFI8216ZQMU](/sequence-files/IGVFFI8216ZQMU/), [IGVFFI7199QJHP](/sequence-files/IGVFFI7199QJHP/), [IGVFFI0644NJFK](/sequence-files/IGVFFI0644NJFK/), [IGVFFI6615TANM](/sequence-files/IGVFFI6615TANM/), [IGVFFI0652NUWH](/sequence-files/IGVFFI0652NUWH/), [IGVFFI6649UNKM](/sequence-files/IGVFFI6649UNKM/), [IGVFFI5141OZWW](/sequence-files/IGVFFI5141OZWW/), [IGVFFI6174LSOD](/sequence-files/IGVFFI6174LSOD/), [IGVFFI2561ASID](/sequence-files/IGVFFI2561ASID/), [IGVFFI2057XHIH](/sequence-files/IGVFFI2057XHIH/), [IGVFFI4712MXWS](/sequence-files/IGVFFI4712MXWS/), [IGVFFI7505UXKC](/sequence-files/IGVFFI7505UXKC/), [IGVFFI9772OERE](/sequence-files/IGVFFI9772OERE/), [IGVFFI8600YLNH](/sequence-files/IGVFFI8600YLNH/), [IGVFFI3930FWVK](/sequence-files/IGVFFI3930FWVK/), [IGVFFI5923YCEK](/sequence-files/IGVFFI5923YCEK/), [IGVFFI3276ZYJY](/sequence-files/IGVFFI3276ZYJY/), [IGVFFI5251YYSC](/sequence-files/IGVFFI5251YYSC/), [IGVFFI5183KSXJ](/sequence-files/IGVFFI5183KSXJ/), [IGVFFI7148OCDR](/sequence-files/IGVFFI7148OCDR/), [IGVFFI6902XXGQ](/sequence-files/IGVFFI6902XXGQ/), [IGVFFI4804JPAP](/sequence-files/IGVFFI4804JPAP/), [IGVFFI4952THYP](/sequence-files/IGVFFI4952THYP/), [IGVFFI1888WELB](/sequence-files/IGVFFI1888WELB/), [IGVFFI6297IFPQ](/sequence-files/IGVFFI6297IFPQ/), [IGVFFI4164XLCG](/sequence-files/IGVFFI4164XLCG/), [IGVFFI0443WSUD](/sequence-files/IGVFFI0443WSUD/), [IGVFFI0869YQBI](/sequence-files/IGVFFI0869YQBI/), [IGVFFI7767OPTV](/sequence-files/IGVFFI7767OPTV/), [IGVFFI2003WWGQ](/sequence-files/IGVFFI2003WWGQ/), [IGVFFI9848UQTT](/sequence-files/IGVFFI9848UQTT/), [IGVFFI3336SXXB](/sequence-files/IGVFFI3336SXXB/) 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/IGVFDS2695EXAH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS2695EXAH](/measurement-sets/IGVFDS2695EXAH/) has sequence file(s): [IGVFFI1756GREJ](/sequence-files/IGVFFI1756GREJ/), [IGVFFI8519TQWA](/sequence-files/IGVFFI8519TQWA/), [IGVFFI9792PHWJ](/sequence-files/IGVFFI9792PHWJ/), [IGVFFI2931SVNR](/sequence-files/IGVFFI2931SVNR/), [IGVFFI1987HBUL](/sequence-files/IGVFFI1987HBUL/), [IGVFFI8399XWTB](/sequence-files/IGVFFI8399XWTB/), [IGVFFI5400CCTJ](/sequence-files/IGVFFI5400CCTJ/), [IGVFFI2420YPWP](/sequence-files/IGVFFI2420YPWP/), [IGVFFI8348CLAQ](/sequence-files/IGVFFI8348CLAQ/), [IGVFFI7433GVOV](/sequence-files/IGVFFI7433GVOV/), [IGVFFI9903DLEC](/sequence-files/IGVFFI9903DLEC/), [IGVFFI8636AMQF](/sequence-files/IGVFFI8636AMQF/), [IGVFFI9086XFBF](/sequence-files/IGVFFI9086XFBF/), [IGVFFI3905WDCB](/sequence-files/IGVFFI3905WDCB/), [IGVFFI4355UMXI](/sequence-files/IGVFFI4355UMXI/), [IGVFFI3438NHNW](/sequence-files/IGVFFI3438NHNW/), [IGVFFI8216ZQMU](/sequence-files/IGVFFI8216ZQMU/), [IGVFFI7199QJHP](/sequence-files/IGVFFI7199QJHP/), [IGVFFI0644NJFK](/sequence-files/IGVFFI0644NJFK/), [IGVFFI6615TANM](/sequence-files/IGVFFI6615TANM/), [IGVFFI0652NUWH](/sequence-files/IGVFFI0652NUWH/), [IGVFFI6649UNKM](/sequence-files/IGVFFI6649UNKM/), [IGVFFI5141OZWW](/sequence-files/IGVFFI5141OZWW/), [IGVFFI6174LSOD](/sequence-files/IGVFFI6174LSOD/), [IGVFFI2561ASID](/sequence-files/IGVFFI2561ASID/), [IGVFFI2057XHIH](/sequence-files/IGVFFI2057XHIH/), [IGVFFI4712MXWS](/sequence-files/IGVFFI4712MXWS/), [IGVFFI7505UXKC](/sequence-files/IGVFFI7505UXKC/), [IGVFFI9772OERE](/sequence-files/IGVFFI9772OERE/), [IGVFFI8600YLNH](/sequence-files/IGVFFI8600YLNH/), [IGVFFI3930FWVK](/sequence-files/IGVFFI3930FWVK/), [IGVFFI5923YCEK](/sequence-files/IGVFFI5923YCEK/), [IGVFFI3276ZYJY](/sequence-files/IGVFFI3276ZYJY/), [IGVFFI5251YYSC](/sequence-files/IGVFFI5251YYSC/), [IGVFFI5183KSXJ](/sequence-files/IGVFFI5183KSXJ/), [IGVFFI7148OCDR](/sequence-files/IGVFFI7148OCDR/), [IGVFFI6902XXGQ](/sequence-files/IGVFFI6902XXGQ/), [IGVFFI4804JPAP](/sequence-files/IGVFFI4804JPAP/), [IGVFFI4952THYP](/sequence-files/IGVFFI4952THYP/), [IGVFFI1888WELB](/sequence-files/IGVFFI1888WELB/), [IGVFFI6297IFPQ](/sequence-files/IGVFFI6297IFPQ/), [IGVFFI4164XLCG](/sequence-files/IGVFFI4164XLCG/), [IGVFFI0443WSUD](/sequence-files/IGVFFI0443WSUD/), [IGVFFI0869YQBI](/sequence-files/IGVFFI0869YQBI/), [IGVFFI7767OPTV](/sequence-files/IGVFFI7767OPTV/), [IGVFFI2003WWGQ](/sequence-files/IGVFFI2003WWGQ/), [IGVFFI9848UQTT](/sequence-files/IGVFFI9848UQTT/), [IGVFFI3336SXXB](/sequence-files/IGVFFI3336SXXB/) 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/IGVFDS2695EXAH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS2695EXAH](/measurement-sets/IGVFDS2695EXAH/) 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/IGVFDS2695EXAH/"
}
]
},
"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": "2024-11-25T23:52:09.457698+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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"accession": "IGVFFI1756GREJ",
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},
{
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},
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},
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},
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},
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},
{
"@id": "/sequence-files/IGVFFI9903DLEC/",
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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 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": "2024-11-26T06:09:58.760979+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": "1c9254ed-64e1-49da-b7c7-17d3a0479f14"
}