IGVFDS7802HNSL

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7802HNSL/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7802HNSL",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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 [IGVFDS7802HNSL](/measurement-sets/IGVFDS7802HNSL/) has sequence file(s) [IGVFFI7299KWPR](/sequence-files/IGVFFI7299KWPR/), [IGVFFI6406JBAQ](/sequence-files/IGVFFI6406JBAQ/), [IGVFFI7586KPPH](/sequence-files/IGVFFI7586KPPH/), [IGVFFI5711RZFA](/sequence-files/IGVFFI5711RZFA/), [IGVFFI1971MRCX](/sequence-files/IGVFFI1971MRCX/), [IGVFFI0411FLCB](/sequence-files/IGVFFI0411FLCB/), [IGVFFI9888SLOH](/sequence-files/IGVFFI9888SLOH/), [IGVFFI5103QKRP](/sequence-files/IGVFFI5103QKRP/), [IGVFFI3758PEJM](/sequence-files/IGVFFI3758PEJM/), [IGVFFI1911LTEB](/sequence-files/IGVFFI1911LTEB/), [IGVFFI0013RDKW](/sequence-files/IGVFFI0013RDKW/), [IGVFFI7077EDPB](/sequence-files/IGVFFI7077EDPB/), [IGVFFI4456CKFH](/sequence-files/IGVFFI4456CKFH/), [IGVFFI0737MCMY](/sequence-files/IGVFFI0737MCMY/), [IGVFFI9881CHIH](/sequence-files/IGVFFI9881CHIH/), [IGVFFI9302YHRV](/sequence-files/IGVFFI9302YHRV/), [IGVFFI4626ZGKL](/sequence-files/IGVFFI4626ZGKL/), [IGVFFI7816KGGY](/sequence-files/IGVFFI7816KGGY/), [IGVFFI7567IUIR](/sequence-files/IGVFFI7567IUIR/), [IGVFFI7317GOFB](/sequence-files/IGVFFI7317GOFB/), [IGVFFI2988OZUW](/sequence-files/IGVFFI2988OZUW/), [IGVFFI7318GYMU](/sequence-files/IGVFFI7318GYMU/), [IGVFFI8533FBMG](/sequence-files/IGVFFI8533FBMG/), [IGVFFI4283AATM](/sequence-files/IGVFFI4283AATM/), [IGVFFI9506GQJB](/sequence-files/IGVFFI9506GQJB/), [IGVFFI5564WCSP](/sequence-files/IGVFFI5564WCSP/), [IGVFFI5166XYMD](/sequence-files/IGVFFI5166XYMD/), [IGVFFI8658IZYS](/sequence-files/IGVFFI8658IZYS/), [IGVFFI3456NAHU](/sequence-files/IGVFFI3456NAHU/), [IGVFFI1536JJLB](/sequence-files/IGVFFI1536JJLB/), [IGVFFI1714XTTB](/sequence-files/IGVFFI1714XTTB/), [IGVFFI1722BGRM](/sequence-files/IGVFFI1722BGRM/), [IGVFFI1770MFRD](/sequence-files/IGVFFI1770MFRD/), [IGVFFI1313IOYF](/sequence-files/IGVFFI1313IOYF/), [IGVFFI0414VEIS](/sequence-files/IGVFFI0414VEIS/), [IGVFFI7283EXSI](/sequence-files/IGVFFI7283EXSI/), [IGVFFI4480IJGV](/sequence-files/IGVFFI4480IJGV/), [IGVFFI2624XOEL](/sequence-files/IGVFFI2624XOEL/), [IGVFFI5972YVTM](/sequence-files/IGVFFI5972YVTM/), [IGVFFI8156XGKE](/sequence-files/IGVFFI8156XGKE/), [IGVFFI3385CEHF](/sequence-files/IGVFFI3385CEHF/), [IGVFFI4698SIPL](/sequence-files/IGVFFI4698SIPL/), [IGVFFI1181DAEX](/sequence-files/IGVFFI1181DAEX/), [IGVFFI8014GSGY](/sequence-files/IGVFFI8014GSGY/), [IGVFFI8544HANM](/sequence-files/IGVFFI8544HANM/), [IGVFFI4092JZVE](/sequence-files/IGVFFI4092JZVE/), [IGVFFI2136HHLB](/sequence-files/IGVFFI2136HHLB/), [IGVFFI8367QWEO](/sequence-files/IGVFFI8367QWEO/) 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/IGVFDS7802HNSL/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7802HNSL](/measurement-sets/IGVFDS7802HNSL/) has sequence file(s): [IGVFFI7299KWPR](/sequence-files/IGVFFI7299KWPR/), [IGVFFI6406JBAQ](/sequence-files/IGVFFI6406JBAQ/), [IGVFFI7586KPPH](/sequence-files/IGVFFI7586KPPH/), [IGVFFI5711RZFA](/sequence-files/IGVFFI5711RZFA/), [IGVFFI1971MRCX](/sequence-files/IGVFFI1971MRCX/), [IGVFFI0411FLCB](/sequence-files/IGVFFI0411FLCB/), [IGVFFI9888SLOH](/sequence-files/IGVFFI9888SLOH/), [IGVFFI5103QKRP](/sequence-files/IGVFFI5103QKRP/), [IGVFFI3758PEJM](/sequence-files/IGVFFI3758PEJM/), [IGVFFI1911LTEB](/sequence-files/IGVFFI1911LTEB/), [IGVFFI0013RDKW](/sequence-files/IGVFFI0013RDKW/), [IGVFFI7077EDPB](/sequence-files/IGVFFI7077EDPB/), [IGVFFI4456CKFH](/sequence-files/IGVFFI4456CKFH/), [IGVFFI0737MCMY](/sequence-files/IGVFFI0737MCMY/), [IGVFFI9881CHIH](/sequence-files/IGVFFI9881CHIH/), [IGVFFI9302YHRV](/sequence-files/IGVFFI9302YHRV/), [IGVFFI4626ZGKL](/sequence-files/IGVFFI4626ZGKL/), [IGVFFI7816KGGY](/sequence-files/IGVFFI7816KGGY/), [IGVFFI7567IUIR](/sequence-files/IGVFFI7567IUIR/), [IGVFFI7317GOFB](/sequence-files/IGVFFI7317GOFB/), [IGVFFI2988OZUW](/sequence-files/IGVFFI2988OZUW/), [IGVFFI7318GYMU](/sequence-files/IGVFFI7318GYMU/), [IGVFFI8533FBMG](/sequence-files/IGVFFI8533FBMG/), [IGVFFI4283AATM](/sequence-files/IGVFFI4283AATM/), [IGVFFI9506GQJB](/sequence-files/IGVFFI9506GQJB/), [IGVFFI5564WCSP](/sequence-files/IGVFFI5564WCSP/), [IGVFFI5166XYMD](/sequence-files/IGVFFI5166XYMD/), [IGVFFI8658IZYS](/sequence-files/IGVFFI8658IZYS/), [IGVFFI3456NAHU](/sequence-files/IGVFFI3456NAHU/), [IGVFFI1536JJLB](/sequence-files/IGVFFI1536JJLB/), [IGVFFI1714XTTB](/sequence-files/IGVFFI1714XTTB/), [IGVFFI1722BGRM](/sequence-files/IGVFFI1722BGRM/), [IGVFFI1770MFRD](/sequence-files/IGVFFI1770MFRD/), [IGVFFI1313IOYF](/sequence-files/IGVFFI1313IOYF/), [IGVFFI0414VEIS](/sequence-files/IGVFFI0414VEIS/), [IGVFFI7283EXSI](/sequence-files/IGVFFI7283EXSI/), [IGVFFI4480IJGV](/sequence-files/IGVFFI4480IJGV/), [IGVFFI2624XOEL](/sequence-files/IGVFFI2624XOEL/), [IGVFFI5972YVTM](/sequence-files/IGVFFI5972YVTM/), [IGVFFI8156XGKE](/sequence-files/IGVFFI8156XGKE/), [IGVFFI3385CEHF](/sequence-files/IGVFFI3385CEHF/), [IGVFFI4698SIPL](/sequence-files/IGVFFI4698SIPL/), [IGVFFI1181DAEX](/sequence-files/IGVFFI1181DAEX/), [IGVFFI8014GSGY](/sequence-files/IGVFFI8014GSGY/), [IGVFFI8544HANM](/sequence-files/IGVFFI8544HANM/), [IGVFFI4092JZVE](/sequence-files/IGVFFI4092JZVE/), [IGVFFI2136HHLB](/sequence-files/IGVFFI2136HHLB/), [IGVFFI8367QWEO](/sequence-files/IGVFFI8367QWEO/) 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/IGVFDS7802HNSL/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7802HNSL](/measurement-sets/IGVFDS7802HNSL/) 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/IGVFDS7802HNSL/"
            }
        ]
    },
    "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": "2024-11-25T23:54:41.648135+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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            "@id": "/sequence-files/IGVFFI7299KWPR/",
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            ],
            "content_type": "reads",
            "controlled_access": false,
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                "status": "released",
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI6406JBAQ/",
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        },
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            "@id": "/sequence-files/IGVFFI7586KPPH/",
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep3_R1"
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            "content_type": "reads",
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        },
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            "@id": "/sequence-files/IGVFFI5711RZFA/",
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        },
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            "@id": "/sequence-files/IGVFFI0411FLCB/",
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        },
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            "@id": "/sequence-files/IGVFFI9888SLOH/",
            "accession": "IGVFFI9888SLOH",
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        },
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            "@id": "/sequence-files/IGVFFI5103QKRP/",
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        },
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            "accession": "IGVFFI3758PEJM",
            "aliases": [
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            ],
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1911LTEB/",
            "accession": "IGVFFI1911LTEB",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T11:19:13.531144+00:00",
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            "upload_status": "validated"
        },
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            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:20:18.034688+00:00",
            "file_format": "fastq",
            "file_size": 8142275,
            "href": "/sequence-files/IGVFFI2136HHLB/@@download/IGVFFI2136HHLB.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/e771c58d-cb5c-4a24-ad67-c5d59e899686/IGVFFI2136HHLB.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-FFrep4-BinD-PCRrep4_S790_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8367QWEO/",
            "accession": "IGVFFI8367QWEO",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinD-PCRrep3_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:18:02.484179+00:00",
            "file_format": "fastq",
            "file_size": 7330352,
            "href": "/sequence-files/IGVFFI8367QWEO/@@download/IGVFFI8367QWEO.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/88db558a-f5cb-4c59-b46a-c3c847dc1985/IGVFFI8367QWEO.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-FFrep4-BinD-PCRrep3_S789_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/IGVFSM5798HMLY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5798HMLY",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-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": "2024-11-26T07:57:26.406807+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": "9cf0a997-0282-4b5f-bf33-a29f44ef615f"
}