{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS8185QENU/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS8185QENU",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-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 [IGVFDS8185QENU](/measurement-sets/IGVFDS8185QENU/) has sequence file(s) [IGVFFI8401WTFP](/sequence-files/IGVFFI8401WTFP/), [IGVFFI2746CRBE](/sequence-files/IGVFFI2746CRBE/), [IGVFFI3694IMFL](/sequence-files/IGVFFI3694IMFL/), [IGVFFI9249GSEU](/sequence-files/IGVFFI9249GSEU/), [IGVFFI1138MWND](/sequence-files/IGVFFI1138MWND/), [IGVFFI8496OFLJ](/sequence-files/IGVFFI8496OFLJ/), [IGVFFI7859FBFT](/sequence-files/IGVFFI7859FBFT/), [IGVFFI2802YEDJ](/sequence-files/IGVFFI2802YEDJ/), [IGVFFI6268DPGY](/sequence-files/IGVFFI6268DPGY/), [IGVFFI6089AYPD](/sequence-files/IGVFFI6089AYPD/), [IGVFFI2672BXYY](/sequence-files/IGVFFI2672BXYY/), [IGVFFI3422SVHQ](/sequence-files/IGVFFI3422SVHQ/), [IGVFFI9792PACX](/sequence-files/IGVFFI9792PACX/), [IGVFFI1143FHZU](/sequence-files/IGVFFI1143FHZU/), [IGVFFI6282NVWU](/sequence-files/IGVFFI6282NVWU/), [IGVFFI7455QLDZ](/sequence-files/IGVFFI7455QLDZ/), [IGVFFI1173AQEB](/sequence-files/IGVFFI1173AQEB/), [IGVFFI2865QDNI](/sequence-files/IGVFFI2865QDNI/), [IGVFFI1852PBRE](/sequence-files/IGVFFI1852PBRE/), [IGVFFI0371LCPO](/sequence-files/IGVFFI0371LCPO/), [IGVFFI5091DCTV](/sequence-files/IGVFFI5091DCTV/), [IGVFFI6660QMFS](/sequence-files/IGVFFI6660QMFS/), [IGVFFI5711MGSB](/sequence-files/IGVFFI5711MGSB/), [IGVFFI9202LPOY](/sequence-files/IGVFFI9202LPOY/), [IGVFFI3478FXNO](/sequence-files/IGVFFI3478FXNO/), [IGVFFI9846HVGF](/sequence-files/IGVFFI9846HVGF/), [IGVFFI6074ABES](/sequence-files/IGVFFI6074ABES/), [IGVFFI9944ABTY](/sequence-files/IGVFFI9944ABTY/), [IGVFFI2655CMOC](/sequence-files/IGVFFI2655CMOC/), [IGVFFI9442SXCT](/sequence-files/IGVFFI9442SXCT/), [IGVFFI4517SDWS](/sequence-files/IGVFFI4517SDWS/), [IGVFFI4044XUSB](/sequence-files/IGVFFI4044XUSB/), [IGVFFI5271ECVR](/sequence-files/IGVFFI5271ECVR/), [IGVFFI7669LPSF](/sequence-files/IGVFFI7669LPSF/), [IGVFFI8029YWBG](/sequence-files/IGVFFI8029YWBG/), [IGVFFI4817PJPD](/sequence-files/IGVFFI4817PJPD/), [IGVFFI4920VQZH](/sequence-files/IGVFFI4920VQZH/), [IGVFFI9424ZQVK](/sequence-files/IGVFFI9424ZQVK/), [IGVFFI6949PXDH](/sequence-files/IGVFFI6949PXDH/), [IGVFFI7719GZIC](/sequence-files/IGVFFI7719GZIC/), [IGVFFI1629AKGJ](/sequence-files/IGVFFI1629AKGJ/), [IGVFFI4014VBDE](/sequence-files/IGVFFI4014VBDE/), [IGVFFI6177QXQP](/sequence-files/IGVFFI6177QXQP/), [IGVFFI0524KRRI](/sequence-files/IGVFFI0524KRRI/), [IGVFFI6753OGBA](/sequence-files/IGVFFI6753OGBA/), [IGVFFI8374EBAA](/sequence-files/IGVFFI8374EBAA/), [IGVFFI3991WYNX](/sequence-files/IGVFFI3991WYNX/), [IGVFFI9553XGVZ](/sequence-files/IGVFFI9553XGVZ/) 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/IGVFDS8185QENU/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS8185QENU](/measurement-sets/IGVFDS8185QENU/) has sequence file(s): [IGVFFI8401WTFP](/sequence-files/IGVFFI8401WTFP/), [IGVFFI2746CRBE](/sequence-files/IGVFFI2746CRBE/), [IGVFFI3694IMFL](/sequence-files/IGVFFI3694IMFL/), [IGVFFI9249GSEU](/sequence-files/IGVFFI9249GSEU/), [IGVFFI1138MWND](/sequence-files/IGVFFI1138MWND/), [IGVFFI8496OFLJ](/sequence-files/IGVFFI8496OFLJ/), [IGVFFI7859FBFT](/sequence-files/IGVFFI7859FBFT/), [IGVFFI2802YEDJ](/sequence-files/IGVFFI2802YEDJ/), [IGVFFI6268DPGY](/sequence-files/IGVFFI6268DPGY/), [IGVFFI6089AYPD](/sequence-files/IGVFFI6089AYPD/), [IGVFFI2672BXYY](/sequence-files/IGVFFI2672BXYY/), [IGVFFI3422SVHQ](/sequence-files/IGVFFI3422SVHQ/), [IGVFFI9792PACX](/sequence-files/IGVFFI9792PACX/), [IGVFFI1143FHZU](/sequence-files/IGVFFI1143FHZU/), [IGVFFI6282NVWU](/sequence-files/IGVFFI6282NVWU/), [IGVFFI7455QLDZ](/sequence-files/IGVFFI7455QLDZ/), [IGVFFI1173AQEB](/sequence-files/IGVFFI1173AQEB/), [IGVFFI2865QDNI](/sequence-files/IGVFFI2865QDNI/), [IGVFFI1852PBRE](/sequence-files/IGVFFI1852PBRE/), [IGVFFI0371LCPO](/sequence-files/IGVFFI0371LCPO/), [IGVFFI5091DCTV](/sequence-files/IGVFFI5091DCTV/), [IGVFFI6660QMFS](/sequence-files/IGVFFI6660QMFS/), [IGVFFI5711MGSB](/sequence-files/IGVFFI5711MGSB/), [IGVFFI9202LPOY](/sequence-files/IGVFFI9202LPOY/), [IGVFFI3478FXNO](/sequence-files/IGVFFI3478FXNO/), [IGVFFI9846HVGF](/sequence-files/IGVFFI9846HVGF/), [IGVFFI6074ABES](/sequence-files/IGVFFI6074ABES/), [IGVFFI9944ABTY](/sequence-files/IGVFFI9944ABTY/), [IGVFFI2655CMOC](/sequence-files/IGVFFI2655CMOC/), [IGVFFI9442SXCT](/sequence-files/IGVFFI9442SXCT/), [IGVFFI4517SDWS](/sequence-files/IGVFFI4517SDWS/), [IGVFFI4044XUSB](/sequence-files/IGVFFI4044XUSB/), [IGVFFI5271ECVR](/sequence-files/IGVFFI5271ECVR/), [IGVFFI7669LPSF](/sequence-files/IGVFFI7669LPSF/), [IGVFFI8029YWBG](/sequence-files/IGVFFI8029YWBG/), [IGVFFI4817PJPD](/sequence-files/IGVFFI4817PJPD/), [IGVFFI4920VQZH](/sequence-files/IGVFFI4920VQZH/), [IGVFFI9424ZQVK](/sequence-files/IGVFFI9424ZQVK/), [IGVFFI6949PXDH](/sequence-files/IGVFFI6949PXDH/), [IGVFFI7719GZIC](/sequence-files/IGVFFI7719GZIC/), [IGVFFI1629AKGJ](/sequence-files/IGVFFI1629AKGJ/), [IGVFFI4014VBDE](/sequence-files/IGVFFI4014VBDE/), [IGVFFI6177QXQP](/sequence-files/IGVFFI6177QXQP/), [IGVFFI0524KRRI](/sequence-files/IGVFFI0524KRRI/), [IGVFFI6753OGBA](/sequence-files/IGVFFI6753OGBA/), [IGVFFI8374EBAA](/sequence-files/IGVFFI8374EBAA/), [IGVFFI3991WYNX](/sequence-files/IGVFFI3991WYNX/), [IGVFFI9553XGVZ](/sequence-files/IGVFFI9553XGVZ/) 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/IGVFDS8185QENU/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS8185QENU](/measurement-sets/IGVFDS8185QENU/) 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/IGVFDS8185QENU/"
}
]
},
"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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{
"@id": "/measurement-sets/IGVFDS4103BJLT/",
"accession": "IGVFDS4103BJLT",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:52:51.438377+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": "IGVFFI8401WTFP",
"aliases": [
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},
{
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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/IGVFFI2672BXYY/",
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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 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": "2024-11-26T06:41:09.443420+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": "3fdd3138-5338-47c6-8341-e6218f3cde04"
}