{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5913KHIA/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5913KHIA",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep3-BinD_AmpliconSequencing"
],
"assay_term": {
"@id": "/assay-terms/OBI_0003661/",
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "mismatched status",
"detail": "Released in vitro system [IGVFSM7851LWAO](/in-vitro-systems/IGVFSM7851LWAO/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_item_status",
"path": "/in-vitro-systems/IGVFSM7851LWAO/"
},
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS5913KHIA](/measurement-sets/IGVFDS5913KHIA/) has sequence file(s) [IGVFFI2156MITI](/sequence-files/IGVFFI2156MITI/), [IGVFFI9825BHGE](/sequence-files/IGVFFI9825BHGE/), [IGVFFI1810TZQV](/sequence-files/IGVFFI1810TZQV/), [IGVFFI3327HAOS](/sequence-files/IGVFFI3327HAOS/), [IGVFFI4316PKDA](/sequence-files/IGVFFI4316PKDA/), [IGVFFI9480YDCO](/sequence-files/IGVFFI9480YDCO/), [IGVFFI4627LCPN](/sequence-files/IGVFFI4627LCPN/), [IGVFFI1558GVUC](/sequence-files/IGVFFI1558GVUC/), [IGVFFI7851RHVZ](/sequence-files/IGVFFI7851RHVZ/), [IGVFFI6386ZUWN](/sequence-files/IGVFFI6386ZUWN/), [IGVFFI5672UYDO](/sequence-files/IGVFFI5672UYDO/), [IGVFFI5294JVMX](/sequence-files/IGVFFI5294JVMX/), [IGVFFI2978PYSU](/sequence-files/IGVFFI2978PYSU/), [IGVFFI7920HFLI](/sequence-files/IGVFFI7920HFLI/), [IGVFFI5818VNBR](/sequence-files/IGVFFI5818VNBR/), [IGVFFI2894ZQGP](/sequence-files/IGVFFI2894ZQGP/), [IGVFFI6655JAPW](/sequence-files/IGVFFI6655JAPW/), [IGVFFI7684KIMI](/sequence-files/IGVFFI7684KIMI/), [IGVFFI8359MZAM](/sequence-files/IGVFFI8359MZAM/), [IGVFFI4463IBNY](/sequence-files/IGVFFI4463IBNY/), [IGVFFI7359WYQF](/sequence-files/IGVFFI7359WYQF/), [IGVFFI1303ZTTN](/sequence-files/IGVFFI1303ZTTN/), [IGVFFI9608GESS](/sequence-files/IGVFFI9608GESS/), [IGVFFI1913FFQJ](/sequence-files/IGVFFI1913FFQJ/), [IGVFFI9486WWEX](/sequence-files/IGVFFI9486WWEX/), [IGVFFI6967WIEV](/sequence-files/IGVFFI6967WIEV/), [IGVFFI1108PSAW](/sequence-files/IGVFFI1108PSAW/), [IGVFFI7341HWPH](/sequence-files/IGVFFI7341HWPH/), [IGVFFI5550ZWCR](/sequence-files/IGVFFI5550ZWCR/), [IGVFFI8253WUCT](/sequence-files/IGVFFI8253WUCT/), [IGVFFI8096EASF](/sequence-files/IGVFFI8096EASF/), [IGVFFI7873OIUE](/sequence-files/IGVFFI7873OIUE/), [IGVFFI4177KYYC](/sequence-files/IGVFFI4177KYYC/), [IGVFFI5087YCLK](/sequence-files/IGVFFI5087YCLK/), [IGVFFI7938MENJ](/sequence-files/IGVFFI7938MENJ/), [IGVFFI5359OUPB](/sequence-files/IGVFFI5359OUPB/), [IGVFFI1752QHPB](/sequence-files/IGVFFI1752QHPB/), [IGVFFI3399PZOV](/sequence-files/IGVFFI3399PZOV/), [IGVFFI3012YXAK](/sequence-files/IGVFFI3012YXAK/), [IGVFFI2241FYTJ](/sequence-files/IGVFFI2241FYTJ/), [IGVFFI3811KSQC](/sequence-files/IGVFFI3811KSQC/), [IGVFFI9468LANJ](/sequence-files/IGVFFI9468LANJ/), [IGVFFI2359IDCS](/sequence-files/IGVFFI2359IDCS/), [IGVFFI3756ANLH](/sequence-files/IGVFFI3756ANLH/), [IGVFFI9807EPBQ](/sequence-files/IGVFFI9807EPBQ/), [IGVFFI5452CYWL](/sequence-files/IGVFFI5452CYWL/), [IGVFFI4421QDTT](/sequence-files/IGVFFI4421QDTT/), [IGVFFI4078ESRZ](/sequence-files/IGVFFI4078ESRZ/) 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/IGVFDS5913KHIA/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5913KHIA](/measurement-sets/IGVFDS5913KHIA/) has sequence file(s): [IGVFFI2156MITI](/sequence-files/IGVFFI2156MITI/), [IGVFFI9825BHGE](/sequence-files/IGVFFI9825BHGE/), [IGVFFI1810TZQV](/sequence-files/IGVFFI1810TZQV/), [IGVFFI3327HAOS](/sequence-files/IGVFFI3327HAOS/), [IGVFFI4316PKDA](/sequence-files/IGVFFI4316PKDA/), [IGVFFI9480YDCO](/sequence-files/IGVFFI9480YDCO/), [IGVFFI4627LCPN](/sequence-files/IGVFFI4627LCPN/), [IGVFFI1558GVUC](/sequence-files/IGVFFI1558GVUC/), [IGVFFI7851RHVZ](/sequence-files/IGVFFI7851RHVZ/), [IGVFFI6386ZUWN](/sequence-files/IGVFFI6386ZUWN/), [IGVFFI5672UYDO](/sequence-files/IGVFFI5672UYDO/), [IGVFFI5294JVMX](/sequence-files/IGVFFI5294JVMX/), [IGVFFI2978PYSU](/sequence-files/IGVFFI2978PYSU/), [IGVFFI7920HFLI](/sequence-files/IGVFFI7920HFLI/), [IGVFFI5818VNBR](/sequence-files/IGVFFI5818VNBR/), [IGVFFI2894ZQGP](/sequence-files/IGVFFI2894ZQGP/), [IGVFFI6655JAPW](/sequence-files/IGVFFI6655JAPW/), [IGVFFI7684KIMI](/sequence-files/IGVFFI7684KIMI/), [IGVFFI8359MZAM](/sequence-files/IGVFFI8359MZAM/), [IGVFFI4463IBNY](/sequence-files/IGVFFI4463IBNY/), [IGVFFI7359WYQF](/sequence-files/IGVFFI7359WYQF/), [IGVFFI1303ZTTN](/sequence-files/IGVFFI1303ZTTN/), [IGVFFI9608GESS](/sequence-files/IGVFFI9608GESS/), [IGVFFI1913FFQJ](/sequence-files/IGVFFI1913FFQJ/), [IGVFFI9486WWEX](/sequence-files/IGVFFI9486WWEX/), [IGVFFI6967WIEV](/sequence-files/IGVFFI6967WIEV/), [IGVFFI1108PSAW](/sequence-files/IGVFFI1108PSAW/), [IGVFFI7341HWPH](/sequence-files/IGVFFI7341HWPH/), [IGVFFI5550ZWCR](/sequence-files/IGVFFI5550ZWCR/), [IGVFFI8253WUCT](/sequence-files/IGVFFI8253WUCT/), [IGVFFI8096EASF](/sequence-files/IGVFFI8096EASF/), [IGVFFI7873OIUE](/sequence-files/IGVFFI7873OIUE/), [IGVFFI4177KYYC](/sequence-files/IGVFFI4177KYYC/), [IGVFFI5087YCLK](/sequence-files/IGVFFI5087YCLK/), [IGVFFI7938MENJ](/sequence-files/IGVFFI7938MENJ/), [IGVFFI5359OUPB](/sequence-files/IGVFFI5359OUPB/), [IGVFFI1752QHPB](/sequence-files/IGVFFI1752QHPB/), [IGVFFI3399PZOV](/sequence-files/IGVFFI3399PZOV/), [IGVFFI3012YXAK](/sequence-files/IGVFFI3012YXAK/), [IGVFFI2241FYTJ](/sequence-files/IGVFFI2241FYTJ/), [IGVFFI3811KSQC](/sequence-files/IGVFFI3811KSQC/), [IGVFFI9468LANJ](/sequence-files/IGVFFI9468LANJ/), [IGVFFI2359IDCS](/sequence-files/IGVFFI2359IDCS/), [IGVFFI3756ANLH](/sequence-files/IGVFFI3756ANLH/), [IGVFFI9807EPBQ](/sequence-files/IGVFFI9807EPBQ/), [IGVFFI5452CYWL](/sequence-files/IGVFFI5452CYWL/), [IGVFFI4421QDTT](/sequence-files/IGVFFI4421QDTT/), [IGVFFI4078ESRZ](/sequence-files/IGVFFI4078ESRZ/) 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/IGVFDS5913KHIA/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5913KHIA](/measurement-sets/IGVFDS5913KHIA/) 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/IGVFDS5913KHIA/"
}
]
},
"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/IGVFDS4869FXYY/",
"accession": "IGVFDS4869FXYY",
"aliases": [
"jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
],
"status": "released"
}
],
"control_for": [],
"creation_timestamp": "2023-12-13T08:48:07.279001+00:00",
"donors": [
{
"@id": "/human-donors/IGVFDO1080XFGV/",
"accession": "IGVFDO1080XFGV",
"aliases": [
"igvf:donor_of_Jurkat"
],
"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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"submitted_files_timestamp": "2023-12-13T09:44:53.986278+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": "42db5731-2679-4fd7-ae14-db542d2a36fb"
}