{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS7736MBPH/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS7736MBPH",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-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 [IGVFDS7736MBPH](/measurement-sets/IGVFDS7736MBPH/) has sequence file(s) [IGVFFI2093NGBY](/sequence-files/IGVFFI2093NGBY/), [IGVFFI9081HFXX](/sequence-files/IGVFFI9081HFXX/), [IGVFFI6461GOHO](/sequence-files/IGVFFI6461GOHO/), [IGVFFI4055EEUB](/sequence-files/IGVFFI4055EEUB/), [IGVFFI9331GFAN](/sequence-files/IGVFFI9331GFAN/), [IGVFFI0938WUTF](/sequence-files/IGVFFI0938WUTF/), [IGVFFI9254GLXJ](/sequence-files/IGVFFI9254GLXJ/), [IGVFFI4134VOBZ](/sequence-files/IGVFFI4134VOBZ/), [IGVFFI4347NZOV](/sequence-files/IGVFFI4347NZOV/), [IGVFFI6191AQNF](/sequence-files/IGVFFI6191AQNF/), [IGVFFI7426HQRC](/sequence-files/IGVFFI7426HQRC/), [IGVFFI0192VESL](/sequence-files/IGVFFI0192VESL/), [IGVFFI8486NDDF](/sequence-files/IGVFFI8486NDDF/), [IGVFFI0727WJTV](/sequence-files/IGVFFI0727WJTV/), [IGVFFI9208EIOG](/sequence-files/IGVFFI9208EIOG/), [IGVFFI4944XBYB](/sequence-files/IGVFFI4944XBYB/), [IGVFFI4065BKMN](/sequence-files/IGVFFI4065BKMN/), [IGVFFI2044QNVW](/sequence-files/IGVFFI2044QNVW/), [IGVFFI6876SPWR](/sequence-files/IGVFFI6876SPWR/), [IGVFFI5888GWHN](/sequence-files/IGVFFI5888GWHN/), [IGVFFI3269APSL](/sequence-files/IGVFFI3269APSL/), [IGVFFI4113YHOE](/sequence-files/IGVFFI4113YHOE/), [IGVFFI0588XKAO](/sequence-files/IGVFFI0588XKAO/), [IGVFFI1853QZBQ](/sequence-files/IGVFFI1853QZBQ/), [IGVFFI5349MEJP](/sequence-files/IGVFFI5349MEJP/), [IGVFFI9890VOOM](/sequence-files/IGVFFI9890VOOM/), [IGVFFI8831WRFP](/sequence-files/IGVFFI8831WRFP/), [IGVFFI1894TWGL](/sequence-files/IGVFFI1894TWGL/), [IGVFFI0521GZDX](/sequence-files/IGVFFI0521GZDX/), [IGVFFI6870QHQP](/sequence-files/IGVFFI6870QHQP/), [IGVFFI6067LRWA](/sequence-files/IGVFFI6067LRWA/), [IGVFFI9579SMJF](/sequence-files/IGVFFI9579SMJF/), [IGVFFI7353AJBK](/sequence-files/IGVFFI7353AJBK/), [IGVFFI4103OHJT](/sequence-files/IGVFFI4103OHJT/), [IGVFFI7869URIW](/sequence-files/IGVFFI7869URIW/), [IGVFFI3669FTGH](/sequence-files/IGVFFI3669FTGH/), [IGVFFI6190VNEW](/sequence-files/IGVFFI6190VNEW/), [IGVFFI0289BZPY](/sequence-files/IGVFFI0289BZPY/), [IGVFFI1788ISAD](/sequence-files/IGVFFI1788ISAD/), [IGVFFI1695WFXJ](/sequence-files/IGVFFI1695WFXJ/), [IGVFFI7429SCRU](/sequence-files/IGVFFI7429SCRU/), [IGVFFI3575ALKI](/sequence-files/IGVFFI3575ALKI/), [IGVFFI0172NLZJ](/sequence-files/IGVFFI0172NLZJ/), [IGVFFI9573UHCR](/sequence-files/IGVFFI9573UHCR/), [IGVFFI1115ORGQ](/sequence-files/IGVFFI1115ORGQ/), [IGVFFI7671WKIH](/sequence-files/IGVFFI7671WKIH/), [IGVFFI9329DHMB](/sequence-files/IGVFFI9329DHMB/), [IGVFFI3711VYFY](/sequence-files/IGVFFI3711VYFY/) 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/IGVFDS7736MBPH/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS7736MBPH](/measurement-sets/IGVFDS7736MBPH/) has sequence file(s): [IGVFFI2093NGBY](/sequence-files/IGVFFI2093NGBY/), [IGVFFI9081HFXX](/sequence-files/IGVFFI9081HFXX/), [IGVFFI6461GOHO](/sequence-files/IGVFFI6461GOHO/), [IGVFFI4055EEUB](/sequence-files/IGVFFI4055EEUB/), [IGVFFI9331GFAN](/sequence-files/IGVFFI9331GFAN/), [IGVFFI0938WUTF](/sequence-files/IGVFFI0938WUTF/), [IGVFFI9254GLXJ](/sequence-files/IGVFFI9254GLXJ/), [IGVFFI4134VOBZ](/sequence-files/IGVFFI4134VOBZ/), [IGVFFI4347NZOV](/sequence-files/IGVFFI4347NZOV/), [IGVFFI6191AQNF](/sequence-files/IGVFFI6191AQNF/), [IGVFFI7426HQRC](/sequence-files/IGVFFI7426HQRC/), [IGVFFI0192VESL](/sequence-files/IGVFFI0192VESL/), [IGVFFI8486NDDF](/sequence-files/IGVFFI8486NDDF/), [IGVFFI0727WJTV](/sequence-files/IGVFFI0727WJTV/), [IGVFFI9208EIOG](/sequence-files/IGVFFI9208EIOG/), [IGVFFI4944XBYB](/sequence-files/IGVFFI4944XBYB/), [IGVFFI4065BKMN](/sequence-files/IGVFFI4065BKMN/), [IGVFFI2044QNVW](/sequence-files/IGVFFI2044QNVW/), [IGVFFI6876SPWR](/sequence-files/IGVFFI6876SPWR/), [IGVFFI5888GWHN](/sequence-files/IGVFFI5888GWHN/), [IGVFFI3269APSL](/sequence-files/IGVFFI3269APSL/), [IGVFFI4113YHOE](/sequence-files/IGVFFI4113YHOE/), [IGVFFI0588XKAO](/sequence-files/IGVFFI0588XKAO/), [IGVFFI1853QZBQ](/sequence-files/IGVFFI1853QZBQ/), [IGVFFI5349MEJP](/sequence-files/IGVFFI5349MEJP/), [IGVFFI9890VOOM](/sequence-files/IGVFFI9890VOOM/), [IGVFFI8831WRFP](/sequence-files/IGVFFI8831WRFP/), [IGVFFI1894TWGL](/sequence-files/IGVFFI1894TWGL/), [IGVFFI0521GZDX](/sequence-files/IGVFFI0521GZDX/), [IGVFFI6870QHQP](/sequence-files/IGVFFI6870QHQP/), [IGVFFI6067LRWA](/sequence-files/IGVFFI6067LRWA/), [IGVFFI9579SMJF](/sequence-files/IGVFFI9579SMJF/), [IGVFFI7353AJBK](/sequence-files/IGVFFI7353AJBK/), [IGVFFI4103OHJT](/sequence-files/IGVFFI4103OHJT/), [IGVFFI7869URIW](/sequence-files/IGVFFI7869URIW/), [IGVFFI3669FTGH](/sequence-files/IGVFFI3669FTGH/), [IGVFFI6190VNEW](/sequence-files/IGVFFI6190VNEW/), [IGVFFI0289BZPY](/sequence-files/IGVFFI0289BZPY/), [IGVFFI1788ISAD](/sequence-files/IGVFFI1788ISAD/), [IGVFFI1695WFXJ](/sequence-files/IGVFFI1695WFXJ/), [IGVFFI7429SCRU](/sequence-files/IGVFFI7429SCRU/), [IGVFFI3575ALKI](/sequence-files/IGVFFI3575ALKI/), [IGVFFI0172NLZJ](/sequence-files/IGVFFI0172NLZJ/), [IGVFFI9573UHCR](/sequence-files/IGVFFI9573UHCR/), [IGVFFI1115ORGQ](/sequence-files/IGVFFI1115ORGQ/), [IGVFFI7671WKIH](/sequence-files/IGVFFI7671WKIH/), [IGVFFI9329DHMB](/sequence-files/IGVFFI9329DHMB/), [IGVFFI3711VYFY](/sequence-files/IGVFFI3711VYFY/) 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/IGVFDS7736MBPH/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS7736MBPH](/measurement-sets/IGVFDS7736MBPH/) 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/IGVFDS7736MBPH/"
}
]
},
"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": "2024-11-25T23:54:11.329993+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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"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": "2024-11-26T07:41:17.976795+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": "4f0ddb08-1059-4c09-9844-01706534ff95"
}