IGVFDS9746QVGD

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS9746QVGD/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9746QVGD",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-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 [IGVFDS9746QVGD](/measurement-sets/IGVFDS9746QVGD/) has sequence file(s) [IGVFFI6817QPHU](/sequence-files/IGVFFI6817QPHU/), [IGVFFI3070ARNB](/sequence-files/IGVFFI3070ARNB/), [IGVFFI9507PNXQ](/sequence-files/IGVFFI9507PNXQ/), [IGVFFI1458COIV](/sequence-files/IGVFFI1458COIV/), [IGVFFI3108NXCH](/sequence-files/IGVFFI3108NXCH/), [IGVFFI6990ZTYO](/sequence-files/IGVFFI6990ZTYO/), [IGVFFI7366DTAL](/sequence-files/IGVFFI7366DTAL/), [IGVFFI6885CJON](/sequence-files/IGVFFI6885CJON/), [IGVFFI4763URXC](/sequence-files/IGVFFI4763URXC/), [IGVFFI7835ULKM](/sequence-files/IGVFFI7835ULKM/), [IGVFFI9337UVFB](/sequence-files/IGVFFI9337UVFB/), [IGVFFI4008IUHG](/sequence-files/IGVFFI4008IUHG/), [IGVFFI4232DESQ](/sequence-files/IGVFFI4232DESQ/), [IGVFFI6519HDDU](/sequence-files/IGVFFI6519HDDU/), [IGVFFI1077PJEO](/sequence-files/IGVFFI1077PJEO/), [IGVFFI1997RAII](/sequence-files/IGVFFI1997RAII/), [IGVFFI0207DIKQ](/sequence-files/IGVFFI0207DIKQ/), [IGVFFI4161URHQ](/sequence-files/IGVFFI4161URHQ/), [IGVFFI2749MOPN](/sequence-files/IGVFFI2749MOPN/), [IGVFFI8231DLZH](/sequence-files/IGVFFI8231DLZH/), [IGVFFI7009DEHM](/sequence-files/IGVFFI7009DEHM/), [IGVFFI8668RXCC](/sequence-files/IGVFFI8668RXCC/), [IGVFFI1127NLNN](/sequence-files/IGVFFI1127NLNN/), [IGVFFI3151HURO](/sequence-files/IGVFFI3151HURO/), [IGVFFI5667NDLO](/sequence-files/IGVFFI5667NDLO/), [IGVFFI6431NIEN](/sequence-files/IGVFFI6431NIEN/), [IGVFFI2221KGNA](/sequence-files/IGVFFI2221KGNA/), [IGVFFI8708CQFD](/sequence-files/IGVFFI8708CQFD/), [IGVFFI2028SBXI](/sequence-files/IGVFFI2028SBXI/), [IGVFFI0347OCUI](/sequence-files/IGVFFI0347OCUI/), [IGVFFI2074PZQA](/sequence-files/IGVFFI2074PZQA/), [IGVFFI7146MRMO](/sequence-files/IGVFFI7146MRMO/), [IGVFFI8567EMRA](/sequence-files/IGVFFI8567EMRA/), [IGVFFI1798VFUW](/sequence-files/IGVFFI1798VFUW/), [IGVFFI2407GGCR](/sequence-files/IGVFFI2407GGCR/), [IGVFFI9845TRGZ](/sequence-files/IGVFFI9845TRGZ/), [IGVFFI1326LCNP](/sequence-files/IGVFFI1326LCNP/), [IGVFFI7244ISCG](/sequence-files/IGVFFI7244ISCG/), [IGVFFI9424TYHU](/sequence-files/IGVFFI9424TYHU/), [IGVFFI0230VONJ](/sequence-files/IGVFFI0230VONJ/), [IGVFFI9976THOF](/sequence-files/IGVFFI9976THOF/), [IGVFFI3228JNPV](/sequence-files/IGVFFI3228JNPV/), [IGVFFI5283JKPS](/sequence-files/IGVFFI5283JKPS/), [IGVFFI7369WTPM](/sequence-files/IGVFFI7369WTPM/), [IGVFFI4731ZCOO](/sequence-files/IGVFFI4731ZCOO/), [IGVFFI6558EBBC](/sequence-files/IGVFFI6558EBBC/), [IGVFFI2839BPHP](/sequence-files/IGVFFI2839BPHP/), [IGVFFI6686VRFZ](/sequence-files/IGVFFI6686VRFZ/) 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/IGVFDS9746QVGD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS9746QVGD](/measurement-sets/IGVFDS9746QVGD/) has sequence file(s): [IGVFFI6817QPHU](/sequence-files/IGVFFI6817QPHU/), [IGVFFI3070ARNB](/sequence-files/IGVFFI3070ARNB/), [IGVFFI9507PNXQ](/sequence-files/IGVFFI9507PNXQ/), [IGVFFI1458COIV](/sequence-files/IGVFFI1458COIV/), [IGVFFI3108NXCH](/sequence-files/IGVFFI3108NXCH/), [IGVFFI6990ZTYO](/sequence-files/IGVFFI6990ZTYO/), [IGVFFI7366DTAL](/sequence-files/IGVFFI7366DTAL/), [IGVFFI6885CJON](/sequence-files/IGVFFI6885CJON/), [IGVFFI4763URXC](/sequence-files/IGVFFI4763URXC/), [IGVFFI7835ULKM](/sequence-files/IGVFFI7835ULKM/), [IGVFFI9337UVFB](/sequence-files/IGVFFI9337UVFB/), [IGVFFI4008IUHG](/sequence-files/IGVFFI4008IUHG/), [IGVFFI4232DESQ](/sequence-files/IGVFFI4232DESQ/), [IGVFFI6519HDDU](/sequence-files/IGVFFI6519HDDU/), [IGVFFI1077PJEO](/sequence-files/IGVFFI1077PJEO/), [IGVFFI1997RAII](/sequence-files/IGVFFI1997RAII/), [IGVFFI0207DIKQ](/sequence-files/IGVFFI0207DIKQ/), [IGVFFI4161URHQ](/sequence-files/IGVFFI4161URHQ/), [IGVFFI2749MOPN](/sequence-files/IGVFFI2749MOPN/), [IGVFFI8231DLZH](/sequence-files/IGVFFI8231DLZH/), [IGVFFI7009DEHM](/sequence-files/IGVFFI7009DEHM/), [IGVFFI8668RXCC](/sequence-files/IGVFFI8668RXCC/), [IGVFFI1127NLNN](/sequence-files/IGVFFI1127NLNN/), [IGVFFI3151HURO](/sequence-files/IGVFFI3151HURO/), [IGVFFI5667NDLO](/sequence-files/IGVFFI5667NDLO/), [IGVFFI6431NIEN](/sequence-files/IGVFFI6431NIEN/), [IGVFFI2221KGNA](/sequence-files/IGVFFI2221KGNA/), [IGVFFI8708CQFD](/sequence-files/IGVFFI8708CQFD/), [IGVFFI2028SBXI](/sequence-files/IGVFFI2028SBXI/), [IGVFFI0347OCUI](/sequence-files/IGVFFI0347OCUI/), [IGVFFI2074PZQA](/sequence-files/IGVFFI2074PZQA/), [IGVFFI7146MRMO](/sequence-files/IGVFFI7146MRMO/), [IGVFFI8567EMRA](/sequence-files/IGVFFI8567EMRA/), [IGVFFI1798VFUW](/sequence-files/IGVFFI1798VFUW/), [IGVFFI2407GGCR](/sequence-files/IGVFFI2407GGCR/), [IGVFFI9845TRGZ](/sequence-files/IGVFFI9845TRGZ/), [IGVFFI1326LCNP](/sequence-files/IGVFFI1326LCNP/), [IGVFFI7244ISCG](/sequence-files/IGVFFI7244ISCG/), [IGVFFI9424TYHU](/sequence-files/IGVFFI9424TYHU/), [IGVFFI0230VONJ](/sequence-files/IGVFFI0230VONJ/), [IGVFFI9976THOF](/sequence-files/IGVFFI9976THOF/), [IGVFFI3228JNPV](/sequence-files/IGVFFI3228JNPV/), [IGVFFI5283JKPS](/sequence-files/IGVFFI5283JKPS/), [IGVFFI7369WTPM](/sequence-files/IGVFFI7369WTPM/), [IGVFFI4731ZCOO](/sequence-files/IGVFFI4731ZCOO/), [IGVFFI6558EBBC](/sequence-files/IGVFFI6558EBBC/), [IGVFFI2839BPHP](/sequence-files/IGVFFI2839BPHP/), [IGVFFI6686VRFZ](/sequence-files/IGVFFI6686VRFZ/) 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/IGVFDS9746QVGD/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS9746QVGD](/measurement-sets/IGVFDS9746QVGD/) 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/IGVFDS9746QVGD/"
            }
        ]
    },
    "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": "2024-11-25T23:53:36.551850+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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            "content_type": "reads",
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        },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9337UVFB/",
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            "s3_uri": "s3://igvf-files/2024/11/26/1f29f6a8-ab63-4876-960c-6c457780d220/IGVFFI2839BPHP.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-FFrep1-BinD-PCRrep10_S652_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6686VRFZ/",
            "accession": "IGVFFI6686VRFZ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-BinD-PCRrep6_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T17:56:46.179843+00:00",
            "file_format": "fastq",
            "file_size": 6490820,
            "href": "/sequence-files/IGVFFI6686VRFZ/@@download/IGVFFI6686VRFZ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/9c9e7c26-86ec-4bdc-86f9-1c199a673147/IGVFFI6686VRFZ.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-FFrep1-BinD-PCRrep6_S648_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/IGVFSM0481TGPS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0481TGPS",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep1-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": "2024-11-26T07:11:46.498661+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": "8fdb6d75-e22f-47a4-b42e-1a60d36517bc"
}