{
"@context": "/terms/",
"@id": "/measurement-sets/IGVFDS5468AKZL/",
"@type": [
"MeasurementSet",
"FileSet",
"Item"
],
"accession": "IGVFDS5468AKZL",
"aliases": [
"jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-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 [IGVFDS5468AKZL](/measurement-sets/IGVFDS5468AKZL/) has sequence file(s) [IGVFFI8520HEJT](/sequence-files/IGVFFI8520HEJT/), [IGVFFI5253QKSJ](/sequence-files/IGVFFI5253QKSJ/), [IGVFFI7171OMSS](/sequence-files/IGVFFI7171OMSS/), [IGVFFI5288EGVZ](/sequence-files/IGVFFI5288EGVZ/), [IGVFFI8137PVGY](/sequence-files/IGVFFI8137PVGY/), [IGVFFI9130YSTL](/sequence-files/IGVFFI9130YSTL/), [IGVFFI1153LXKV](/sequence-files/IGVFFI1153LXKV/), [IGVFFI9982UTUZ](/sequence-files/IGVFFI9982UTUZ/), [IGVFFI4141RLDU](/sequence-files/IGVFFI4141RLDU/), [IGVFFI1121SZUE](/sequence-files/IGVFFI1121SZUE/), [IGVFFI4136DONA](/sequence-files/IGVFFI4136DONA/), [IGVFFI7848FJZX](/sequence-files/IGVFFI7848FJZX/), [IGVFFI4942EXFU](/sequence-files/IGVFFI4942EXFU/), [IGVFFI1479LNUG](/sequence-files/IGVFFI1479LNUG/), [IGVFFI9065PRQP](/sequence-files/IGVFFI9065PRQP/), [IGVFFI9416VYNM](/sequence-files/IGVFFI9416VYNM/), [IGVFFI4867CFWY](/sequence-files/IGVFFI4867CFWY/), [IGVFFI2650KVIO](/sequence-files/IGVFFI2650KVIO/), [IGVFFI0561RNMU](/sequence-files/IGVFFI0561RNMU/), [IGVFFI3756DQYO](/sequence-files/IGVFFI3756DQYO/), [IGVFFI2924CZRT](/sequence-files/IGVFFI2924CZRT/), [IGVFFI6280HWXC](/sequence-files/IGVFFI6280HWXC/), [IGVFFI7775OINY](/sequence-files/IGVFFI7775OINY/), [IGVFFI4253SKSJ](/sequence-files/IGVFFI4253SKSJ/), [IGVFFI7385XAWU](/sequence-files/IGVFFI7385XAWU/), [IGVFFI6804LUEE](/sequence-files/IGVFFI6804LUEE/), [IGVFFI1141QPJE](/sequence-files/IGVFFI1141QPJE/), [IGVFFI7823SJBJ](/sequence-files/IGVFFI7823SJBJ/), [IGVFFI1042YCNE](/sequence-files/IGVFFI1042YCNE/), [IGVFFI5899PTWQ](/sequence-files/IGVFFI5899PTWQ/), [IGVFFI2843IYMC](/sequence-files/IGVFFI2843IYMC/), [IGVFFI1430XHUA](/sequence-files/IGVFFI1430XHUA/), [IGVFFI0209INLN](/sequence-files/IGVFFI0209INLN/), [IGVFFI1927NVAA](/sequence-files/IGVFFI1927NVAA/), [IGVFFI9696HUBU](/sequence-files/IGVFFI9696HUBU/), [IGVFFI2875OOBR](/sequence-files/IGVFFI2875OOBR/), [IGVFFI3066QRJG](/sequence-files/IGVFFI3066QRJG/), [IGVFFI3966FNWL](/sequence-files/IGVFFI3966FNWL/), [IGVFFI3027WOVJ](/sequence-files/IGVFFI3027WOVJ/), [IGVFFI7707NSGE](/sequence-files/IGVFFI7707NSGE/), [IGVFFI6046WPTU](/sequence-files/IGVFFI6046WPTU/), [IGVFFI3035XEKM](/sequence-files/IGVFFI3035XEKM/), [IGVFFI5445GTJS](/sequence-files/IGVFFI5445GTJS/), [IGVFFI1564JHHP](/sequence-files/IGVFFI1564JHHP/), [IGVFFI1920KTTG](/sequence-files/IGVFFI1920KTTG/), [IGVFFI5657BXLV](/sequence-files/IGVFFI5657BXLV/), [IGVFFI2458OPDJ](/sequence-files/IGVFFI2458OPDJ/), [IGVFFI4911AKWJ](/sequence-files/IGVFFI4911AKWJ/) 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/IGVFDS5468AKZL/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS5468AKZL](/measurement-sets/IGVFDS5468AKZL/) has sequence file(s): [IGVFFI8520HEJT](/sequence-files/IGVFFI8520HEJT/), [IGVFFI5253QKSJ](/sequence-files/IGVFFI5253QKSJ/), [IGVFFI7171OMSS](/sequence-files/IGVFFI7171OMSS/), [IGVFFI5288EGVZ](/sequence-files/IGVFFI5288EGVZ/), [IGVFFI8137PVGY](/sequence-files/IGVFFI8137PVGY/), [IGVFFI9130YSTL](/sequence-files/IGVFFI9130YSTL/), [IGVFFI1153LXKV](/sequence-files/IGVFFI1153LXKV/), [IGVFFI9982UTUZ](/sequence-files/IGVFFI9982UTUZ/), [IGVFFI4141RLDU](/sequence-files/IGVFFI4141RLDU/), [IGVFFI1121SZUE](/sequence-files/IGVFFI1121SZUE/), [IGVFFI4136DONA](/sequence-files/IGVFFI4136DONA/), [IGVFFI7848FJZX](/sequence-files/IGVFFI7848FJZX/), [IGVFFI4942EXFU](/sequence-files/IGVFFI4942EXFU/), [IGVFFI1479LNUG](/sequence-files/IGVFFI1479LNUG/), [IGVFFI9065PRQP](/sequence-files/IGVFFI9065PRQP/), [IGVFFI9416VYNM](/sequence-files/IGVFFI9416VYNM/), [IGVFFI4867CFWY](/sequence-files/IGVFFI4867CFWY/), [IGVFFI2650KVIO](/sequence-files/IGVFFI2650KVIO/), [IGVFFI0561RNMU](/sequence-files/IGVFFI0561RNMU/), [IGVFFI3756DQYO](/sequence-files/IGVFFI3756DQYO/), [IGVFFI2924CZRT](/sequence-files/IGVFFI2924CZRT/), [IGVFFI6280HWXC](/sequence-files/IGVFFI6280HWXC/), [IGVFFI7775OINY](/sequence-files/IGVFFI7775OINY/), [IGVFFI4253SKSJ](/sequence-files/IGVFFI4253SKSJ/), [IGVFFI7385XAWU](/sequence-files/IGVFFI7385XAWU/), [IGVFFI6804LUEE](/sequence-files/IGVFFI6804LUEE/), [IGVFFI1141QPJE](/sequence-files/IGVFFI1141QPJE/), [IGVFFI7823SJBJ](/sequence-files/IGVFFI7823SJBJ/), [IGVFFI1042YCNE](/sequence-files/IGVFFI1042YCNE/), [IGVFFI5899PTWQ](/sequence-files/IGVFFI5899PTWQ/), [IGVFFI2843IYMC](/sequence-files/IGVFFI2843IYMC/), [IGVFFI1430XHUA](/sequence-files/IGVFFI1430XHUA/), [IGVFFI0209INLN](/sequence-files/IGVFFI0209INLN/), [IGVFFI1927NVAA](/sequence-files/IGVFFI1927NVAA/), [IGVFFI9696HUBU](/sequence-files/IGVFFI9696HUBU/), [IGVFFI2875OOBR](/sequence-files/IGVFFI2875OOBR/), [IGVFFI3066QRJG](/sequence-files/IGVFFI3066QRJG/), [IGVFFI3966FNWL](/sequence-files/IGVFFI3966FNWL/), [IGVFFI3027WOVJ](/sequence-files/IGVFFI3027WOVJ/), [IGVFFI7707NSGE](/sequence-files/IGVFFI7707NSGE/), [IGVFFI6046WPTU](/sequence-files/IGVFFI6046WPTU/), [IGVFFI3035XEKM](/sequence-files/IGVFFI3035XEKM/), [IGVFFI5445GTJS](/sequence-files/IGVFFI5445GTJS/), [IGVFFI1564JHHP](/sequence-files/IGVFFI1564JHHP/), [IGVFFI1920KTTG](/sequence-files/IGVFFI1920KTTG/), [IGVFFI5657BXLV](/sequence-files/IGVFFI5657BXLV/), [IGVFFI2458OPDJ](/sequence-files/IGVFFI2458OPDJ/), [IGVFFI4911AKWJ](/sequence-files/IGVFFI4911AKWJ/) 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/IGVFDS5468AKZL/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS5468AKZL](/measurement-sets/IGVFDS5468AKZL/) 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/IGVFDS5468AKZL/"
}
]
},
"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": [
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],
"status": "preview"
}
],
"control_for": [],
"creation_timestamp": "2024-11-25T23:54:32.807713+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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},
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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": "2024-11-26T07:56:44.256568+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": "a9264d7e-758e-49e6-afe5-6d12a18a6bb9"
}