IGVFDS2992ZYJE

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2992ZYJE/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2992ZYJE",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-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 [IGVFDS2992ZYJE](/measurement-sets/IGVFDS2992ZYJE/) has sequence file(s) [IGVFFI5158WENW](/sequence-files/IGVFFI5158WENW/), [IGVFFI6091XEVG](/sequence-files/IGVFFI6091XEVG/), [IGVFFI6312XFTX](/sequence-files/IGVFFI6312XFTX/), [IGVFFI7684VJOE](/sequence-files/IGVFFI7684VJOE/), [IGVFFI5882HZGD](/sequence-files/IGVFFI5882HZGD/), [IGVFFI5748UDPG](/sequence-files/IGVFFI5748UDPG/), [IGVFFI5718IKFV](/sequence-files/IGVFFI5718IKFV/), [IGVFFI7007RKYR](/sequence-files/IGVFFI7007RKYR/), [IGVFFI0962TPFL](/sequence-files/IGVFFI0962TPFL/), [IGVFFI2155OGKD](/sequence-files/IGVFFI2155OGKD/), [IGVFFI4540ACGI](/sequence-files/IGVFFI4540ACGI/), [IGVFFI5804NHKR](/sequence-files/IGVFFI5804NHKR/), [IGVFFI7643SVBR](/sequence-files/IGVFFI7643SVBR/), [IGVFFI1716BJMA](/sequence-files/IGVFFI1716BJMA/), [IGVFFI9344CJZO](/sequence-files/IGVFFI9344CJZO/), [IGVFFI0143SIGA](/sequence-files/IGVFFI0143SIGA/), [IGVFFI2747TDHZ](/sequence-files/IGVFFI2747TDHZ/), [IGVFFI3675PVPY](/sequence-files/IGVFFI3675PVPY/), [IGVFFI5858XJSJ](/sequence-files/IGVFFI5858XJSJ/), [IGVFFI8111ZSUM](/sequence-files/IGVFFI8111ZSUM/), [IGVFFI2671SGZS](/sequence-files/IGVFFI2671SGZS/), [IGVFFI5800IRJK](/sequence-files/IGVFFI5800IRJK/), [IGVFFI4076DKOG](/sequence-files/IGVFFI4076DKOG/), [IGVFFI3665HZWQ](/sequence-files/IGVFFI3665HZWQ/), [IGVFFI1727JGUG](/sequence-files/IGVFFI1727JGUG/), [IGVFFI2860SPFC](/sequence-files/IGVFFI2860SPFC/), [IGVFFI9746AWSX](/sequence-files/IGVFFI9746AWSX/), [IGVFFI9958LTCL](/sequence-files/IGVFFI9958LTCL/), [IGVFFI6356WTUR](/sequence-files/IGVFFI6356WTUR/), [IGVFFI9822JHMY](/sequence-files/IGVFFI9822JHMY/), [IGVFFI1386CKHM](/sequence-files/IGVFFI1386CKHM/), [IGVFFI7488ORWF](/sequence-files/IGVFFI7488ORWF/), [IGVFFI9946OHNJ](/sequence-files/IGVFFI9946OHNJ/), [IGVFFI2073RXYM](/sequence-files/IGVFFI2073RXYM/), [IGVFFI9550HSUI](/sequence-files/IGVFFI9550HSUI/), [IGVFFI1269WYEF](/sequence-files/IGVFFI1269WYEF/), [IGVFFI5961MGOJ](/sequence-files/IGVFFI5961MGOJ/), [IGVFFI9391QDHD](/sequence-files/IGVFFI9391QDHD/), [IGVFFI6294ZNIN](/sequence-files/IGVFFI6294ZNIN/), [IGVFFI6256JNXO](/sequence-files/IGVFFI6256JNXO/), [IGVFFI2143RDEJ](/sequence-files/IGVFFI2143RDEJ/), [IGVFFI5081HCQN](/sequence-files/IGVFFI5081HCQN/), [IGVFFI6873FIHK](/sequence-files/IGVFFI6873FIHK/), [IGVFFI3545IFGL](/sequence-files/IGVFFI3545IFGL/), [IGVFFI5399GQNC](/sequence-files/IGVFFI5399GQNC/), [IGVFFI5157KASC](/sequence-files/IGVFFI5157KASC/), [IGVFFI6627YPTH](/sequence-files/IGVFFI6627YPTH/), [IGVFFI4048ZSOP](/sequence-files/IGVFFI4048ZSOP/) 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/IGVFDS2992ZYJE/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2992ZYJE](/measurement-sets/IGVFDS2992ZYJE/) has sequence file(s): [IGVFFI5158WENW](/sequence-files/IGVFFI5158WENW/), [IGVFFI6091XEVG](/sequence-files/IGVFFI6091XEVG/), [IGVFFI6312XFTX](/sequence-files/IGVFFI6312XFTX/), [IGVFFI7684VJOE](/sequence-files/IGVFFI7684VJOE/), [IGVFFI5882HZGD](/sequence-files/IGVFFI5882HZGD/), [IGVFFI5748UDPG](/sequence-files/IGVFFI5748UDPG/), [IGVFFI5718IKFV](/sequence-files/IGVFFI5718IKFV/), [IGVFFI7007RKYR](/sequence-files/IGVFFI7007RKYR/), [IGVFFI0962TPFL](/sequence-files/IGVFFI0962TPFL/), [IGVFFI2155OGKD](/sequence-files/IGVFFI2155OGKD/), [IGVFFI4540ACGI](/sequence-files/IGVFFI4540ACGI/), [IGVFFI5804NHKR](/sequence-files/IGVFFI5804NHKR/), [IGVFFI7643SVBR](/sequence-files/IGVFFI7643SVBR/), [IGVFFI1716BJMA](/sequence-files/IGVFFI1716BJMA/), [IGVFFI9344CJZO](/sequence-files/IGVFFI9344CJZO/), [IGVFFI0143SIGA](/sequence-files/IGVFFI0143SIGA/), [IGVFFI2747TDHZ](/sequence-files/IGVFFI2747TDHZ/), [IGVFFI3675PVPY](/sequence-files/IGVFFI3675PVPY/), [IGVFFI5858XJSJ](/sequence-files/IGVFFI5858XJSJ/), [IGVFFI8111ZSUM](/sequence-files/IGVFFI8111ZSUM/), [IGVFFI2671SGZS](/sequence-files/IGVFFI2671SGZS/), [IGVFFI5800IRJK](/sequence-files/IGVFFI5800IRJK/), [IGVFFI4076DKOG](/sequence-files/IGVFFI4076DKOG/), [IGVFFI3665HZWQ](/sequence-files/IGVFFI3665HZWQ/), [IGVFFI1727JGUG](/sequence-files/IGVFFI1727JGUG/), [IGVFFI2860SPFC](/sequence-files/IGVFFI2860SPFC/), [IGVFFI9746AWSX](/sequence-files/IGVFFI9746AWSX/), [IGVFFI9958LTCL](/sequence-files/IGVFFI9958LTCL/), [IGVFFI6356WTUR](/sequence-files/IGVFFI6356WTUR/), [IGVFFI9822JHMY](/sequence-files/IGVFFI9822JHMY/), [IGVFFI1386CKHM](/sequence-files/IGVFFI1386CKHM/), [IGVFFI7488ORWF](/sequence-files/IGVFFI7488ORWF/), [IGVFFI9946OHNJ](/sequence-files/IGVFFI9946OHNJ/), [IGVFFI2073RXYM](/sequence-files/IGVFFI2073RXYM/), [IGVFFI9550HSUI](/sequence-files/IGVFFI9550HSUI/), [IGVFFI1269WYEF](/sequence-files/IGVFFI1269WYEF/), [IGVFFI5961MGOJ](/sequence-files/IGVFFI5961MGOJ/), [IGVFFI9391QDHD](/sequence-files/IGVFFI9391QDHD/), [IGVFFI6294ZNIN](/sequence-files/IGVFFI6294ZNIN/), [IGVFFI6256JNXO](/sequence-files/IGVFFI6256JNXO/), [IGVFFI2143RDEJ](/sequence-files/IGVFFI2143RDEJ/), [IGVFFI5081HCQN](/sequence-files/IGVFFI5081HCQN/), [IGVFFI6873FIHK](/sequence-files/IGVFFI6873FIHK/), [IGVFFI3545IFGL](/sequence-files/IGVFFI3545IFGL/), [IGVFFI5399GQNC](/sequence-files/IGVFFI5399GQNC/), [IGVFFI5157KASC](/sequence-files/IGVFFI5157KASC/), [IGVFFI6627YPTH](/sequence-files/IGVFFI6627YPTH/), [IGVFFI4048ZSOP](/sequence-files/IGVFFI4048ZSOP/) 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/IGVFDS2992ZYJE/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS2992ZYJE](/measurement-sets/IGVFDS2992ZYJE/) 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/IGVFDS2992ZYJE/"
            }
        ]
    },
    "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": "2024-11-25T23:54:21.615834+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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            "upload_status": "validated"
        },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6312XFTX/",
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        },
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            "@id": "/sequence-files/IGVFFI5718IKFV/",
            "accession": "IGVFFI5718IKFV",
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        },
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            "@id": "/sequence-files/IGVFFI7007RKYR/",
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        },
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            "aliases": [
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI2155OGKD/",
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            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinD-PCRrep2_R1"
            ],
            "content_type": "reads",
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            "upload_status": "validated"
        },
        {
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinD-PCRrep5_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:53:04.084254+00:00",
            "file_format": "fastq",
            "file_size": 6380358,
            "href": "/sequence-files/IGVFFI6627YPTH/@@download/IGVFFI6627YPTH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/d824c4da-91e4-4250-a076-f432bcbca228/IGVFFI6627YPTH.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-FFrep3-BinD-PCRrep5_S743_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4048ZSOP/",
            "accession": "IGVFFI4048ZSOP",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinD-PCRrep12_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:09:50.406340+00:00",
            "file_format": "fastq",
            "file_size": 6333404,
            "href": "/sequence-files/IGVFFI4048ZSOP/@@download/IGVFFI4048ZSOP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/a583800e-226e-4ecf-b750-738503790b5a/IGVFFI4048ZSOP.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-FFrep3-BinD-PCRrep12_S750_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/IGVFSM3785MWIW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3785MWIW",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-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": "2024-11-26T07:41:52.081499+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": "ada81a01-804f-40ad-8de7-bd7285fc16ab"
}