IGVFDS5030BFVD

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5030BFVD/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5030BFVD",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-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 [IGVFDS5030BFVD](/measurement-sets/IGVFDS5030BFVD/) has sequence file(s) [IGVFFI9290WKPF](/sequence-files/IGVFFI9290WKPF/), [IGVFFI5555YFSA](/sequence-files/IGVFFI5555YFSA/), [IGVFFI7470XGQR](/sequence-files/IGVFFI7470XGQR/), [IGVFFI8016OQXD](/sequence-files/IGVFFI8016OQXD/), [IGVFFI6656RRTV](/sequence-files/IGVFFI6656RRTV/), [IGVFFI6334JMKD](/sequence-files/IGVFFI6334JMKD/), [IGVFFI4557FVUP](/sequence-files/IGVFFI4557FVUP/), [IGVFFI3577AOVS](/sequence-files/IGVFFI3577AOVS/), [IGVFFI1941CISV](/sequence-files/IGVFFI1941CISV/), [IGVFFI1100OAWK](/sequence-files/IGVFFI1100OAWK/), [IGVFFI2121WHPB](/sequence-files/IGVFFI2121WHPB/), [IGVFFI7886NUJW](/sequence-files/IGVFFI7886NUJW/), [IGVFFI2418OOXC](/sequence-files/IGVFFI2418OOXC/), [IGVFFI6313GOKF](/sequence-files/IGVFFI6313GOKF/), [IGVFFI5231YNBK](/sequence-files/IGVFFI5231YNBK/), [IGVFFI5853CTQO](/sequence-files/IGVFFI5853CTQO/), [IGVFFI0348TBPT](/sequence-files/IGVFFI0348TBPT/), [IGVFFI4768VZDM](/sequence-files/IGVFFI4768VZDM/), [IGVFFI6943GJJU](/sequence-files/IGVFFI6943GJJU/), [IGVFFI6075XHOQ](/sequence-files/IGVFFI6075XHOQ/), [IGVFFI1215VFEK](/sequence-files/IGVFFI1215VFEK/), [IGVFFI9207WCMM](/sequence-files/IGVFFI9207WCMM/), [IGVFFI6487XTKL](/sequence-files/IGVFFI6487XTKL/), [IGVFFI3107PTQG](/sequence-files/IGVFFI3107PTQG/), [IGVFFI7795YIVM](/sequence-files/IGVFFI7795YIVM/), [IGVFFI1242YYXC](/sequence-files/IGVFFI1242YYXC/), [IGVFFI3891FEWF](/sequence-files/IGVFFI3891FEWF/), [IGVFFI1275XZCE](/sequence-files/IGVFFI1275XZCE/), [IGVFFI6446LVFA](/sequence-files/IGVFFI6446LVFA/), [IGVFFI9021FYDO](/sequence-files/IGVFFI9021FYDO/), [IGVFFI3758GZVO](/sequence-files/IGVFFI3758GZVO/), [IGVFFI4142UUWV](/sequence-files/IGVFFI4142UUWV/), [IGVFFI8830OFKG](/sequence-files/IGVFFI8830OFKG/), [IGVFFI7653ORSL](/sequence-files/IGVFFI7653ORSL/), [IGVFFI8974XRNU](/sequence-files/IGVFFI8974XRNU/), [IGVFFI1954UBWL](/sequence-files/IGVFFI1954UBWL/), [IGVFFI0214EYUU](/sequence-files/IGVFFI0214EYUU/), [IGVFFI1210KRMB](/sequence-files/IGVFFI1210KRMB/), [IGVFFI6374WPSN](/sequence-files/IGVFFI6374WPSN/), [IGVFFI2446EKSA](/sequence-files/IGVFFI2446EKSA/), [IGVFFI8389RLWN](/sequence-files/IGVFFI8389RLWN/), [IGVFFI4211WSIN](/sequence-files/IGVFFI4211WSIN/), [IGVFFI4720ILLC](/sequence-files/IGVFFI4720ILLC/), [IGVFFI1491EMCM](/sequence-files/IGVFFI1491EMCM/), [IGVFFI2809DCKZ](/sequence-files/IGVFFI2809DCKZ/), [IGVFFI6037YNJB](/sequence-files/IGVFFI6037YNJB/), [IGVFFI7851TPKE](/sequence-files/IGVFFI7851TPKE/), [IGVFFI9494ITNK](/sequence-files/IGVFFI9494ITNK/) 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/IGVFDS5030BFVD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5030BFVD](/measurement-sets/IGVFDS5030BFVD/) has sequence file(s): [IGVFFI9290WKPF](/sequence-files/IGVFFI9290WKPF/), [IGVFFI5555YFSA](/sequence-files/IGVFFI5555YFSA/), [IGVFFI7470XGQR](/sequence-files/IGVFFI7470XGQR/), [IGVFFI8016OQXD](/sequence-files/IGVFFI8016OQXD/), [IGVFFI6656RRTV](/sequence-files/IGVFFI6656RRTV/), [IGVFFI6334JMKD](/sequence-files/IGVFFI6334JMKD/), [IGVFFI4557FVUP](/sequence-files/IGVFFI4557FVUP/), [IGVFFI3577AOVS](/sequence-files/IGVFFI3577AOVS/), [IGVFFI1941CISV](/sequence-files/IGVFFI1941CISV/), [IGVFFI1100OAWK](/sequence-files/IGVFFI1100OAWK/), [IGVFFI2121WHPB](/sequence-files/IGVFFI2121WHPB/), [IGVFFI7886NUJW](/sequence-files/IGVFFI7886NUJW/), [IGVFFI2418OOXC](/sequence-files/IGVFFI2418OOXC/), [IGVFFI6313GOKF](/sequence-files/IGVFFI6313GOKF/), [IGVFFI5231YNBK](/sequence-files/IGVFFI5231YNBK/), [IGVFFI5853CTQO](/sequence-files/IGVFFI5853CTQO/), [IGVFFI0348TBPT](/sequence-files/IGVFFI0348TBPT/), [IGVFFI4768VZDM](/sequence-files/IGVFFI4768VZDM/), [IGVFFI6943GJJU](/sequence-files/IGVFFI6943GJJU/), [IGVFFI6075XHOQ](/sequence-files/IGVFFI6075XHOQ/), [IGVFFI1215VFEK](/sequence-files/IGVFFI1215VFEK/), [IGVFFI9207WCMM](/sequence-files/IGVFFI9207WCMM/), [IGVFFI6487XTKL](/sequence-files/IGVFFI6487XTKL/), [IGVFFI3107PTQG](/sequence-files/IGVFFI3107PTQG/), [IGVFFI7795YIVM](/sequence-files/IGVFFI7795YIVM/), [IGVFFI1242YYXC](/sequence-files/IGVFFI1242YYXC/), [IGVFFI3891FEWF](/sequence-files/IGVFFI3891FEWF/), [IGVFFI1275XZCE](/sequence-files/IGVFFI1275XZCE/), [IGVFFI6446LVFA](/sequence-files/IGVFFI6446LVFA/), [IGVFFI9021FYDO](/sequence-files/IGVFFI9021FYDO/), [IGVFFI3758GZVO](/sequence-files/IGVFFI3758GZVO/), [IGVFFI4142UUWV](/sequence-files/IGVFFI4142UUWV/), [IGVFFI8830OFKG](/sequence-files/IGVFFI8830OFKG/), [IGVFFI7653ORSL](/sequence-files/IGVFFI7653ORSL/), [IGVFFI8974XRNU](/sequence-files/IGVFFI8974XRNU/), [IGVFFI1954UBWL](/sequence-files/IGVFFI1954UBWL/), [IGVFFI0214EYUU](/sequence-files/IGVFFI0214EYUU/), [IGVFFI1210KRMB](/sequence-files/IGVFFI1210KRMB/), [IGVFFI6374WPSN](/sequence-files/IGVFFI6374WPSN/), [IGVFFI2446EKSA](/sequence-files/IGVFFI2446EKSA/), [IGVFFI8389RLWN](/sequence-files/IGVFFI8389RLWN/), [IGVFFI4211WSIN](/sequence-files/IGVFFI4211WSIN/), [IGVFFI4720ILLC](/sequence-files/IGVFFI4720ILLC/), [IGVFFI1491EMCM](/sequence-files/IGVFFI1491EMCM/), [IGVFFI2809DCKZ](/sequence-files/IGVFFI2809DCKZ/), [IGVFFI6037YNJB](/sequence-files/IGVFFI6037YNJB/), [IGVFFI7851TPKE](/sequence-files/IGVFFI7851TPKE/), [IGVFFI9494ITNK](/sequence-files/IGVFFI9494ITNK/) 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/IGVFDS5030BFVD/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5030BFVD](/measurement-sets/IGVFDS5030BFVD/) 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/IGVFDS5030BFVD/"
            }
        ]
    },
    "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": "2024-11-25T23:53:16.043518+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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            "@id": "/sequence-files/IGVFFI9290WKPF/",
            "accession": "IGVFFI9290WKPF",
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            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T06:57:30.404874+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"
        },
        {
            "@id": "/sequence-files/IGVFFI5555YFSA/",
            "accession": "IGVFFI5555YFSA",
            "aliases": [
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            ],
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7470XGQR/",
            "accession": "IGVFFI7470XGQR",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep7_R1"
            ],
            "content_type": "reads",
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            "upload_status": "validated"
        },
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        },
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            "@id": "/sequence-files/IGVFFI6656RRTV/",
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            },
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        },
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            "@id": "/sequence-files/IGVFFI6334JMKD/",
            "accession": "IGVFFI6334JMKD",
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep8_R1"
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4557FVUP/",
            "accession": "IGVFFI4557FVUP",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep12_R1"
            ],
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            "creation_timestamp": "2024-11-26T07:10:36.245010+00:00",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3577AOVS/",
            "accession": "IGVFFI3577AOVS",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep1_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2024-11-26T06:56:02.318582+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1941CISV/",
            "accession": "IGVFFI1941CISV",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep6_R1"
            ],
            "content_type": "reads",
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                "term_name": "Illumina NovaSeq X"
            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1100OAWK/",
            "accession": "IGVFFI1100OAWK",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep3_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T06:58:55.907666+00:00",
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            },
            "status": "preview",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2121WHPB/",
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            "creation_timestamp": "2024-11-26T17:24:03.721512+00:00",
            "file_format": "fastq",
            "file_size": 6693550,
            "href": "/sequence-files/IGVFFI7851TPKE/@@download/IGVFFI7851TPKE.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/e09abe59-3563-479f-b453-f815b25e98c6/IGVFFI7851TPKE.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-BioRep1-FFrep4-BinD-PCRrep5_S599_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9494ITNK/",
            "accession": "IGVFFI9494ITNK",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinD-PCRrep6_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T17:26:30.709625+00:00",
            "file_format": "fastq",
            "file_size": 8665186,
            "href": "/sequence-files/IGVFFI9494ITNK/@@download/IGVFFI9494ITNK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/299bd4d7-56fb-4573-925d-38ed1231a8ee/IGVFFI9494ITNK.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-BioRep1-FFrep4-BinD-PCRrep6_S600_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/IGVFSM1648EHGD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1648EHGD",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-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": "2024-11-26T06:56:02.318582+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": "55229b94-0eda-473c-b2be-c3a386cf55c0"
}