{
"@context": "/terms/",
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"MeasurementSet",
"FileSet",
"Item"
],
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"aliases": [
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],
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"@id": "/assay-terms/OBI_0003661/",
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],
"status": "released",
"term_name": "in vitro CRISPR screen using flow cytometry"
},
"audit": {
"INTERNAL_ACTION": [
{
"category": "missing sequencing kit",
"detail": "Measurement set [IGVFDS1096VFTG](/measurement-sets/IGVFDS1096VFTG/) has sequence file(s) [IGVFFI0344BHMW](/sequence-files/IGVFFI0344BHMW/), [IGVFFI0448RNXB](/sequence-files/IGVFFI0448RNXB/), [IGVFFI9220YDMK](/sequence-files/IGVFFI9220YDMK/), [IGVFFI4142JHCK](/sequence-files/IGVFFI4142JHCK/), [IGVFFI8085OPEI](/sequence-files/IGVFFI8085OPEI/), [IGVFFI4840JNRU](/sequence-files/IGVFFI4840JNRU/), [IGVFFI6144WZOA](/sequence-files/IGVFFI6144WZOA/), [IGVFFI8798HMNI](/sequence-files/IGVFFI8798HMNI/), [IGVFFI5407HEHJ](/sequence-files/IGVFFI5407HEHJ/), [IGVFFI9963SXBC](/sequence-files/IGVFFI9963SXBC/), [IGVFFI9693IBQE](/sequence-files/IGVFFI9693IBQE/), [IGVFFI0826WGHJ](/sequence-files/IGVFFI0826WGHJ/), [IGVFFI8168RBDT](/sequence-files/IGVFFI8168RBDT/), [IGVFFI7154HURZ](/sequence-files/IGVFFI7154HURZ/), [IGVFFI8291BKZP](/sequence-files/IGVFFI8291BKZP/), [IGVFFI8732OGMN](/sequence-files/IGVFFI8732OGMN/) which lack specification of a `sequencing_kit`. Sequence files in a file set associated wtih bulk data should specify a sequencing kit.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_inconsistent_sequencing_kit",
"path": "/measurement-sets/IGVFDS1096VFTG/"
},
{
"category": "missing sequence specification",
"detail": "Measurement set [IGVFDS1096VFTG](/measurement-sets/IGVFDS1096VFTG/) has sequence file(s): [IGVFFI0344BHMW](/sequence-files/IGVFFI0344BHMW/), [IGVFFI0448RNXB](/sequence-files/IGVFFI0448RNXB/), [IGVFFI9220YDMK](/sequence-files/IGVFFI9220YDMK/), [IGVFFI4142JHCK](/sequence-files/IGVFFI4142JHCK/), [IGVFFI8085OPEI](/sequence-files/IGVFFI8085OPEI/), [IGVFFI4840JNRU](/sequence-files/IGVFFI4840JNRU/), [IGVFFI6144WZOA](/sequence-files/IGVFFI6144WZOA/), [IGVFFI8798HMNI](/sequence-files/IGVFFI8798HMNI/), [IGVFFI5407HEHJ](/sequence-files/IGVFFI5407HEHJ/), [IGVFFI9963SXBC](/sequence-files/IGVFFI9963SXBC/), [IGVFFI9693IBQE](/sequence-files/IGVFFI9693IBQE/), [IGVFFI0826WGHJ](/sequence-files/IGVFFI0826WGHJ/), [IGVFFI8168RBDT](/sequence-files/IGVFFI8168RBDT/), [IGVFFI7154HURZ](/sequence-files/IGVFFI7154HURZ/), [IGVFFI8291BKZP](/sequence-files/IGVFFI8291BKZP/), [IGVFFI8732OGMN](/sequence-files/IGVFFI8732OGMN/) which do not have any `seqspecs`. Sequence files in a file set associated with bulk data are expected to link to a sequence specification file.",
"level": 30,
"level_name": "INTERNAL_ACTION",
"name": "audit_missing_seqspec",
"path": "/measurement-sets/IGVFDS1096VFTG/"
}
],
"WARNING": [
{
"category": "missing auxiliary set",
"detail": "Measurement set [IGVFDS1096VFTG](/measurement-sets/IGVFDS1096VFTG/) 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/IGVFDS1096VFTG/"
}
]
},
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},
"title": "Stanford Center for Connecting DNA Variants to Function and Phenotype"
},
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinB-PCRrep2_S888_I2_001.fastq.gz",
"upload_status": "validated"
},
{
"@id": "/sequence-files/IGVFFI8732OGMN/",
"accession": "IGVFFI8732OGMN",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-BinB-PCRrep1_I2"
],
"content_type": "reads",
"controlled_access": false,
"creation_timestamp": "2024-12-12T00:10:32.852282+00:00",
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"sequencing_platform": {
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"status": "released",
"term_name": "Illumina NovaSeq X"
},
"status": "preview",
"submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C12-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinB-PCRrep1_S876_I2_001.fastq.gz",
"upload_status": "validated"
}
],
"input_for": [
"/analysis-sets/IGVFDS8174BPPS/"
],
"lab": {
"@id": "/labs/jesse-engreitz/",
"title": "Jesse Engreitz, Stanford"
},
"preferred_assay_title": "Variant-EFFECTS",
"protocols": [
"https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
],
"samples": [
{
"@id": "/in-vitro-systems/IGVFSM9431CHMK/",
"@type": [
"InVitroSystem",
"Biosample",
"Sample",
"Item"
],
"accession": "IGVFSM9431CHMK",
"aliases": [
"jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCAG-THP1-BioRep1-FFrep1-BinB"
],
"classifications": [
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],
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"modifications": [
{
"@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
"modality": "prime editing",
"status": "released"
}
],
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{
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"@type": [
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"OntologyTerm",
"Item"
],
"aliases": [
"igvf:THP-1"
],
"status": "released",
"summary": "THP-1",
"term_name": "THP-1"
}
],
"status": "preview",
"summary": "Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library",
"taxa": "Homo sapiens"
}
],
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"title": "Michael Montgomery"
},
"submitted_files_timestamp": "2024-12-11T01:44:57.255261+00:00",
"summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": [
"PPIase F",
"peptidylprolyl isomerase F",
"Cyp-D",
"peptidyl-prolyl cis-trans isomerase F, mitochondrial",
"PPIF",
"CyP-M",
"cyclophilin F",
"peptidyl-prolyl cis-trans isomerase, mitochondrial",
"cyclophilin 3",
"cyclophilin D",
"rotamase F",
"mitochondrial cyclophilin",
"CypD",
"CYP3"
]
}
],
"uuid": "bf511e8a-6448-45e1-98b9-7fd1cb92fb94"
}