IGVFDS8782KHRJ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8782KHRJ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8782KHRJ",
    "aliases": [
        "jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinB_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 [IGVFSM2181BEKF](/in-vitro-systems/IGVFSM2181BEKF/) 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/IGVFSM2181BEKF/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS8782KHRJ](/measurement-sets/IGVFDS8782KHRJ/) has sequence file(s) [IGVFFI4273LOIP](/sequence-files/IGVFFI4273LOIP/), [IGVFFI3133YOXP](/sequence-files/IGVFFI3133YOXP/), [IGVFFI3343IOCF](/sequence-files/IGVFFI3343IOCF/), [IGVFFI4799JDBO](/sequence-files/IGVFFI4799JDBO/), [IGVFFI4070WLOA](/sequence-files/IGVFFI4070WLOA/), [IGVFFI8857XOGP](/sequence-files/IGVFFI8857XOGP/), [IGVFFI5829KRCX](/sequence-files/IGVFFI5829KRCX/), [IGVFFI9144MQFL](/sequence-files/IGVFFI9144MQFL/), [IGVFFI8707JMVM](/sequence-files/IGVFFI8707JMVM/), [IGVFFI8632GQZJ](/sequence-files/IGVFFI8632GQZJ/), [IGVFFI5368AJWA](/sequence-files/IGVFFI5368AJWA/), [IGVFFI2080KORO](/sequence-files/IGVFFI2080KORO/), [IGVFFI9576JIGE](/sequence-files/IGVFFI9576JIGE/), [IGVFFI0564ZSPY](/sequence-files/IGVFFI0564ZSPY/), [IGVFFI3676ZFWX](/sequence-files/IGVFFI3676ZFWX/), [IGVFFI0927MEVY](/sequence-files/IGVFFI0927MEVY/), [IGVFFI3245GGFN](/sequence-files/IGVFFI3245GGFN/), [IGVFFI9141IFTT](/sequence-files/IGVFFI9141IFTT/), [IGVFFI2045QXGB](/sequence-files/IGVFFI2045QXGB/), [IGVFFI0767OCUM](/sequence-files/IGVFFI0767OCUM/), [IGVFFI1236ETZW](/sequence-files/IGVFFI1236ETZW/), [IGVFFI7898BHEJ](/sequence-files/IGVFFI7898BHEJ/), [IGVFFI0810JDHU](/sequence-files/IGVFFI0810JDHU/), [IGVFFI3008JMEQ](/sequence-files/IGVFFI3008JMEQ/), [IGVFFI7559USND](/sequence-files/IGVFFI7559USND/), [IGVFFI3583LXZN](/sequence-files/IGVFFI3583LXZN/), [IGVFFI6173XWJJ](/sequence-files/IGVFFI6173XWJJ/), [IGVFFI5947WRYM](/sequence-files/IGVFFI5947WRYM/), [IGVFFI6852DZEU](/sequence-files/IGVFFI6852DZEU/), [IGVFFI2266OLMK](/sequence-files/IGVFFI2266OLMK/), [IGVFFI2840IDLR](/sequence-files/IGVFFI2840IDLR/), [IGVFFI9517XYGY](/sequence-files/IGVFFI9517XYGY/), [IGVFFI4368VHVO](/sequence-files/IGVFFI4368VHVO/), [IGVFFI8277MANK](/sequence-files/IGVFFI8277MANK/), [IGVFFI7748RUUE](/sequence-files/IGVFFI7748RUUE/), [IGVFFI4263IVOQ](/sequence-files/IGVFFI4263IVOQ/), [IGVFFI0920TLXK](/sequence-files/IGVFFI0920TLXK/), [IGVFFI2320YWUN](/sequence-files/IGVFFI2320YWUN/), [IGVFFI0233NMTO](/sequence-files/IGVFFI0233NMTO/), [IGVFFI5194LQTT](/sequence-files/IGVFFI5194LQTT/), [IGVFFI3579XEQR](/sequence-files/IGVFFI3579XEQR/), [IGVFFI1428DKAX](/sequence-files/IGVFFI1428DKAX/), [IGVFFI0251RLLU](/sequence-files/IGVFFI0251RLLU/), [IGVFFI1267TXVN](/sequence-files/IGVFFI1267TXVN/), [IGVFFI7622RETL](/sequence-files/IGVFFI7622RETL/), [IGVFFI5545JZBQ](/sequence-files/IGVFFI5545JZBQ/), [IGVFFI5532SCGV](/sequence-files/IGVFFI5532SCGV/), [IGVFFI7729UUFF](/sequence-files/IGVFFI7729UUFF/) 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/IGVFDS8782KHRJ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8782KHRJ](/measurement-sets/IGVFDS8782KHRJ/) has sequence file(s): [IGVFFI4273LOIP](/sequence-files/IGVFFI4273LOIP/), [IGVFFI3133YOXP](/sequence-files/IGVFFI3133YOXP/), [IGVFFI3343IOCF](/sequence-files/IGVFFI3343IOCF/), [IGVFFI4799JDBO](/sequence-files/IGVFFI4799JDBO/), [IGVFFI4070WLOA](/sequence-files/IGVFFI4070WLOA/), [IGVFFI8857XOGP](/sequence-files/IGVFFI8857XOGP/), [IGVFFI5829KRCX](/sequence-files/IGVFFI5829KRCX/), [IGVFFI9144MQFL](/sequence-files/IGVFFI9144MQFL/), [IGVFFI8707JMVM](/sequence-files/IGVFFI8707JMVM/), [IGVFFI8632GQZJ](/sequence-files/IGVFFI8632GQZJ/), [IGVFFI5368AJWA](/sequence-files/IGVFFI5368AJWA/), [IGVFFI2080KORO](/sequence-files/IGVFFI2080KORO/), [IGVFFI9576JIGE](/sequence-files/IGVFFI9576JIGE/), [IGVFFI0564ZSPY](/sequence-files/IGVFFI0564ZSPY/), [IGVFFI3676ZFWX](/sequence-files/IGVFFI3676ZFWX/), [IGVFFI0927MEVY](/sequence-files/IGVFFI0927MEVY/), [IGVFFI3245GGFN](/sequence-files/IGVFFI3245GGFN/), [IGVFFI9141IFTT](/sequence-files/IGVFFI9141IFTT/), [IGVFFI2045QXGB](/sequence-files/IGVFFI2045QXGB/), [IGVFFI0767OCUM](/sequence-files/IGVFFI0767OCUM/), [IGVFFI1236ETZW](/sequence-files/IGVFFI1236ETZW/), [IGVFFI7898BHEJ](/sequence-files/IGVFFI7898BHEJ/), [IGVFFI0810JDHU](/sequence-files/IGVFFI0810JDHU/), [IGVFFI3008JMEQ](/sequence-files/IGVFFI3008JMEQ/), [IGVFFI7559USND](/sequence-files/IGVFFI7559USND/), [IGVFFI3583LXZN](/sequence-files/IGVFFI3583LXZN/), [IGVFFI6173XWJJ](/sequence-files/IGVFFI6173XWJJ/), [IGVFFI5947WRYM](/sequence-files/IGVFFI5947WRYM/), [IGVFFI6852DZEU](/sequence-files/IGVFFI6852DZEU/), [IGVFFI2266OLMK](/sequence-files/IGVFFI2266OLMK/), [IGVFFI2840IDLR](/sequence-files/IGVFFI2840IDLR/), [IGVFFI9517XYGY](/sequence-files/IGVFFI9517XYGY/), [IGVFFI4368VHVO](/sequence-files/IGVFFI4368VHVO/), [IGVFFI8277MANK](/sequence-files/IGVFFI8277MANK/), [IGVFFI7748RUUE](/sequence-files/IGVFFI7748RUUE/), [IGVFFI4263IVOQ](/sequence-files/IGVFFI4263IVOQ/), [IGVFFI0920TLXK](/sequence-files/IGVFFI0920TLXK/), [IGVFFI2320YWUN](/sequence-files/IGVFFI2320YWUN/), [IGVFFI0233NMTO](/sequence-files/IGVFFI0233NMTO/), [IGVFFI5194LQTT](/sequence-files/IGVFFI5194LQTT/), [IGVFFI3579XEQR](/sequence-files/IGVFFI3579XEQR/), [IGVFFI1428DKAX](/sequence-files/IGVFFI1428DKAX/), [IGVFFI0251RLLU](/sequence-files/IGVFFI0251RLLU/), [IGVFFI1267TXVN](/sequence-files/IGVFFI1267TXVN/), [IGVFFI7622RETL](/sequence-files/IGVFFI7622RETL/), [IGVFFI5545JZBQ](/sequence-files/IGVFFI5545JZBQ/), [IGVFFI5532SCGV](/sequence-files/IGVFFI5532SCGV/), [IGVFFI7729UUFF](/sequence-files/IGVFFI7729UUFF/) 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/IGVFDS8782KHRJ/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS8782KHRJ](/measurement-sets/IGVFDS8782KHRJ/) 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/IGVFDS8782KHRJ/"
            }
        ]
    },
    "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/",
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                "jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-Jurkat-PE2_Exp2_NegControl_AmpliconSequencing"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-12-13T08:48:04.835932+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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            "s3_uri": "s3://igvf-files/2023/12/13/f5e5edea-b3bb-42b9-be25-5ed1a8f754ea/IGVFFI7729UUFF.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "230423pPPIFEnformerJurkat-Jurkat-PE-pPPIF_Enformer-Amp-pPPIF-BioRep1-FFRep2_BinB-PCRrep7_S67_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS6299IJHG/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This measurement set previously used Variant FlowFISH as a preferred_assay_title, but this enum is now removed. So it has been defaulted to Variant-EFFECTS.",
    "preferred_assay_title": "Variant-EFFECTS",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "release_timestamp": "2023-12-20T23:08:56.371156+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2181BEKF/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2181BEKF",
            "aliases": [
                "jesse-engreitz:230423pPPIFEnformer-Jurkat-Amp_PPIF_promoter-BioRep1-FFrep2-BinB"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2385DHZO/",
                    "accession": "IGVFDS2385DHZO",
                    "file_set_type": "guide library",
                    "status": "in progress",
                    "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_0002796/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:Jurkat"
                    ],
                    "status": "released",
                    "summary": "Jurkat",
                    "term_name": "Jurkat"
                }
            ],
            "status": "released",
            "summary": "Jurkat 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": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-13T09:36:38.264170+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": "5930f2df-4703-431e-b641-f643117fbff4"
}