IGVFDS8140CVHC

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8140CVHC/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8140CVHC",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinD_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 [IGVFDS8140CVHC](/measurement-sets/IGVFDS8140CVHC/) has sequence file(s) [IGVFFI6428ASMD](/sequence-files/IGVFFI6428ASMD/), [IGVFFI8157OULG](/sequence-files/IGVFFI8157OULG/), [IGVFFI6809JRGD](/sequence-files/IGVFFI6809JRGD/), [IGVFFI9362HYLG](/sequence-files/IGVFFI9362HYLG/), [IGVFFI7313JVVE](/sequence-files/IGVFFI7313JVVE/), [IGVFFI9016VPZQ](/sequence-files/IGVFFI9016VPZQ/), [IGVFFI5540IZAL](/sequence-files/IGVFFI5540IZAL/), [IGVFFI5821PYWA](/sequence-files/IGVFFI5821PYWA/), [IGVFFI5613KGYN](/sequence-files/IGVFFI5613KGYN/), [IGVFFI6458IOHE](/sequence-files/IGVFFI6458IOHE/), [IGVFFI0227XYOF](/sequence-files/IGVFFI0227XYOF/), [IGVFFI8353YRSQ](/sequence-files/IGVFFI8353YRSQ/), [IGVFFI0260WMST](/sequence-files/IGVFFI0260WMST/), [IGVFFI0990LGVI](/sequence-files/IGVFFI0990LGVI/), [IGVFFI4020BZOP](/sequence-files/IGVFFI4020BZOP/), [IGVFFI6407EHEO](/sequence-files/IGVFFI6407EHEO/), [IGVFFI6002MOYI](/sequence-files/IGVFFI6002MOYI/), [IGVFFI9068IBQZ](/sequence-files/IGVFFI9068IBQZ/), [IGVFFI8694OBZP](/sequence-files/IGVFFI8694OBZP/), [IGVFFI7015MDGE](/sequence-files/IGVFFI7015MDGE/), [IGVFFI4590NONZ](/sequence-files/IGVFFI4590NONZ/), [IGVFFI3300DKXY](/sequence-files/IGVFFI3300DKXY/), [IGVFFI1071MHIA](/sequence-files/IGVFFI1071MHIA/), [IGVFFI2192CMAY](/sequence-files/IGVFFI2192CMAY/), [IGVFFI9691XGXE](/sequence-files/IGVFFI9691XGXE/), [IGVFFI1382MLGP](/sequence-files/IGVFFI1382MLGP/), [IGVFFI3336EEZE](/sequence-files/IGVFFI3336EEZE/), [IGVFFI4306IFAM](/sequence-files/IGVFFI4306IFAM/), [IGVFFI5828XVUW](/sequence-files/IGVFFI5828XVUW/), [IGVFFI2834HNMV](/sequence-files/IGVFFI2834HNMV/), [IGVFFI3277PJPD](/sequence-files/IGVFFI3277PJPD/), [IGVFFI5652HUDO](/sequence-files/IGVFFI5652HUDO/), [IGVFFI9859VMOM](/sequence-files/IGVFFI9859VMOM/), [IGVFFI4737TJFJ](/sequence-files/IGVFFI4737TJFJ/), [IGVFFI7338UFMM](/sequence-files/IGVFFI7338UFMM/), [IGVFFI1818WLHH](/sequence-files/IGVFFI1818WLHH/), [IGVFFI5823HKTU](/sequence-files/IGVFFI5823HKTU/), [IGVFFI4148HHRK](/sequence-files/IGVFFI4148HHRK/), [IGVFFI4038NFBR](/sequence-files/IGVFFI4038NFBR/), [IGVFFI9591KMKC](/sequence-files/IGVFFI9591KMKC/), [IGVFFI7600XPBY](/sequence-files/IGVFFI7600XPBY/), [IGVFFI2027RAHP](/sequence-files/IGVFFI2027RAHP/), [IGVFFI6009TZZD](/sequence-files/IGVFFI6009TZZD/), [IGVFFI1108QODX](/sequence-files/IGVFFI1108QODX/), [IGVFFI1807TBXX](/sequence-files/IGVFFI1807TBXX/), [IGVFFI0843MQMI](/sequence-files/IGVFFI0843MQMI/), [IGVFFI1363RKHE](/sequence-files/IGVFFI1363RKHE/), [IGVFFI7103IFTR](/sequence-files/IGVFFI7103IFTR/) 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/IGVFDS8140CVHC/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8140CVHC](/measurement-sets/IGVFDS8140CVHC/) has sequence file(s): [IGVFFI6428ASMD](/sequence-files/IGVFFI6428ASMD/), [IGVFFI8157OULG](/sequence-files/IGVFFI8157OULG/), [IGVFFI6809JRGD](/sequence-files/IGVFFI6809JRGD/), [IGVFFI9362HYLG](/sequence-files/IGVFFI9362HYLG/), [IGVFFI7313JVVE](/sequence-files/IGVFFI7313JVVE/), [IGVFFI9016VPZQ](/sequence-files/IGVFFI9016VPZQ/), [IGVFFI5540IZAL](/sequence-files/IGVFFI5540IZAL/), [IGVFFI5821PYWA](/sequence-files/IGVFFI5821PYWA/), [IGVFFI5613KGYN](/sequence-files/IGVFFI5613KGYN/), [IGVFFI6458IOHE](/sequence-files/IGVFFI6458IOHE/), [IGVFFI0227XYOF](/sequence-files/IGVFFI0227XYOF/), [IGVFFI8353YRSQ](/sequence-files/IGVFFI8353YRSQ/), [IGVFFI0260WMST](/sequence-files/IGVFFI0260WMST/), [IGVFFI0990LGVI](/sequence-files/IGVFFI0990LGVI/), [IGVFFI4020BZOP](/sequence-files/IGVFFI4020BZOP/), [IGVFFI6407EHEO](/sequence-files/IGVFFI6407EHEO/), [IGVFFI6002MOYI](/sequence-files/IGVFFI6002MOYI/), [IGVFFI9068IBQZ](/sequence-files/IGVFFI9068IBQZ/), [IGVFFI8694OBZP](/sequence-files/IGVFFI8694OBZP/), [IGVFFI7015MDGE](/sequence-files/IGVFFI7015MDGE/), [IGVFFI4590NONZ](/sequence-files/IGVFFI4590NONZ/), [IGVFFI3300DKXY](/sequence-files/IGVFFI3300DKXY/), [IGVFFI1071MHIA](/sequence-files/IGVFFI1071MHIA/), [IGVFFI2192CMAY](/sequence-files/IGVFFI2192CMAY/), [IGVFFI9691XGXE](/sequence-files/IGVFFI9691XGXE/), [IGVFFI1382MLGP](/sequence-files/IGVFFI1382MLGP/), [IGVFFI3336EEZE](/sequence-files/IGVFFI3336EEZE/), [IGVFFI4306IFAM](/sequence-files/IGVFFI4306IFAM/), [IGVFFI5828XVUW](/sequence-files/IGVFFI5828XVUW/), [IGVFFI2834HNMV](/sequence-files/IGVFFI2834HNMV/), [IGVFFI3277PJPD](/sequence-files/IGVFFI3277PJPD/), [IGVFFI5652HUDO](/sequence-files/IGVFFI5652HUDO/), [IGVFFI9859VMOM](/sequence-files/IGVFFI9859VMOM/), [IGVFFI4737TJFJ](/sequence-files/IGVFFI4737TJFJ/), [IGVFFI7338UFMM](/sequence-files/IGVFFI7338UFMM/), [IGVFFI1818WLHH](/sequence-files/IGVFFI1818WLHH/), [IGVFFI5823HKTU](/sequence-files/IGVFFI5823HKTU/), [IGVFFI4148HHRK](/sequence-files/IGVFFI4148HHRK/), [IGVFFI4038NFBR](/sequence-files/IGVFFI4038NFBR/), [IGVFFI9591KMKC](/sequence-files/IGVFFI9591KMKC/), [IGVFFI7600XPBY](/sequence-files/IGVFFI7600XPBY/), [IGVFFI2027RAHP](/sequence-files/IGVFFI2027RAHP/), [IGVFFI6009TZZD](/sequence-files/IGVFFI6009TZZD/), [IGVFFI1108QODX](/sequence-files/IGVFFI1108QODX/), [IGVFFI1807TBXX](/sequence-files/IGVFFI1807TBXX/), [IGVFFI0843MQMI](/sequence-files/IGVFFI0843MQMI/), [IGVFFI1363RKHE](/sequence-files/IGVFFI1363RKHE/), [IGVFFI7103IFTR](/sequence-files/IGVFFI7103IFTR/) 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/IGVFDS8140CVHC/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS8140CVHC](/measurement-sets/IGVFDS8140CVHC/) 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/IGVFDS8140CVHC/"
            }
        ]
    },
    "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"
    },
    "control_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4103BJLT/",
            "accession": "IGVFDS4103BJLT",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
            ],
            "status": "preview"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-11-25T23:53:57.891939+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",
    "files": [
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            "accession": "IGVFFI6428ASMD",
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            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:26:20.075029+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI8157OULG/",
            "accession": "IGVFFI8157OULG",
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            ],
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI6809JRGD/",
            "accession": "IGVFFI6809JRGD",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinD-PCRrep12_R1"
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        },
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            "@id": "/sequence-files/IGVFFI9362HYLG/",
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        },
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        },
        {
            "@id": "/sequence-files/IGVFFI5540IZAL/",
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            ],
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        },
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            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinD-PCRrep2_R1"
            ],
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6458IOHE/",
            "accession": "IGVFFI6458IOHE",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinD-PCRrep4_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:31:08.079102+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0227XYOF/",
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            "href": "/sequence-files/IGVFFI1363RKHE/@@download/IGVFFI1363RKHE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/a45a0e4c-52d0-4f80-8e25-f3a0a3cfa5f9/IGVFFI1363RKHE.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep2-BinD-PCRrep12_S702_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7103IFTR/",
            "accession": "IGVFFI7103IFTR",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinD-PCRrep7_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:28:32.964800+00:00",
            "file_format": "fastq",
            "file_size": 7669366,
            "href": "/sequence-files/IGVFFI7103IFTR/@@download/IGVFFI7103IFTR.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/81287768-ece2-440a-a229-070f0f271734/IGVFFI7103IFTR.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep2-FFrep2-BinD-PCRrep7_S697_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4833ZRTZ/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "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"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9180KDGZ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9180KDGZ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinD"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@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 76-100% 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": "2024-11-26T07:26:20.075029+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": "6c7e99d3-3130-47c4-bac2-785e4183fbd1"
}