IGVFDS8230NTUC

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8230NTUC/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8230NTUC",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinB_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 [IGVFDS8230NTUC](/measurement-sets/IGVFDS8230NTUC/) has sequence file(s) [IGVFFI1638QNHU](/sequence-files/IGVFFI1638QNHU/), [IGVFFI8172TTYS](/sequence-files/IGVFFI8172TTYS/), [IGVFFI0061YGQF](/sequence-files/IGVFFI0061YGQF/), [IGVFFI3686ZRQS](/sequence-files/IGVFFI3686ZRQS/), [IGVFFI6949GTER](/sequence-files/IGVFFI6949GTER/), [IGVFFI3279TAQE](/sequence-files/IGVFFI3279TAQE/), [IGVFFI8727IKUM](/sequence-files/IGVFFI8727IKUM/), [IGVFFI7827ZTZF](/sequence-files/IGVFFI7827ZTZF/), [IGVFFI6144MQEY](/sequence-files/IGVFFI6144MQEY/), [IGVFFI4281XRDL](/sequence-files/IGVFFI4281XRDL/), [IGVFFI2270TQZD](/sequence-files/IGVFFI2270TQZD/), [IGVFFI2208XXCI](/sequence-files/IGVFFI2208XXCI/), [IGVFFI5200YQBH](/sequence-files/IGVFFI5200YQBH/), [IGVFFI8366PMMG](/sequence-files/IGVFFI8366PMMG/), [IGVFFI7627ZADE](/sequence-files/IGVFFI7627ZADE/), [IGVFFI6692FXTI](/sequence-files/IGVFFI6692FXTI/), [IGVFFI9001SWZI](/sequence-files/IGVFFI9001SWZI/), [IGVFFI0822KFZB](/sequence-files/IGVFFI0822KFZB/), [IGVFFI0598DIFH](/sequence-files/IGVFFI0598DIFH/), [IGVFFI1052WTYQ](/sequence-files/IGVFFI1052WTYQ/), [IGVFFI9217FRPG](/sequence-files/IGVFFI9217FRPG/), [IGVFFI9341OMBK](/sequence-files/IGVFFI9341OMBK/), [IGVFFI9733FYOF](/sequence-files/IGVFFI9733FYOF/), [IGVFFI6982IYEP](/sequence-files/IGVFFI6982IYEP/), [IGVFFI8307AIRB](/sequence-files/IGVFFI8307AIRB/), [IGVFFI7017LKDP](/sequence-files/IGVFFI7017LKDP/), [IGVFFI0108HSLI](/sequence-files/IGVFFI0108HSLI/), [IGVFFI7081DOTN](/sequence-files/IGVFFI7081DOTN/), [IGVFFI7866CQDH](/sequence-files/IGVFFI7866CQDH/), [IGVFFI6560YHHV](/sequence-files/IGVFFI6560YHHV/), [IGVFFI9378LDZC](/sequence-files/IGVFFI9378LDZC/), [IGVFFI1538CDMZ](/sequence-files/IGVFFI1538CDMZ/), [IGVFFI5728SDMD](/sequence-files/IGVFFI5728SDMD/), [IGVFFI8518JZNQ](/sequence-files/IGVFFI8518JZNQ/), [IGVFFI9741PXPZ](/sequence-files/IGVFFI9741PXPZ/), [IGVFFI7848COEW](/sequence-files/IGVFFI7848COEW/), [IGVFFI7703LMEB](/sequence-files/IGVFFI7703LMEB/), [IGVFFI2462RXKB](/sequence-files/IGVFFI2462RXKB/), [IGVFFI6712QPAZ](/sequence-files/IGVFFI6712QPAZ/), [IGVFFI0296XPVN](/sequence-files/IGVFFI0296XPVN/), [IGVFFI9092XYMC](/sequence-files/IGVFFI9092XYMC/), [IGVFFI0243XBSC](/sequence-files/IGVFFI0243XBSC/), [IGVFFI6371GIAC](/sequence-files/IGVFFI6371GIAC/), [IGVFFI9636RTHI](/sequence-files/IGVFFI9636RTHI/), [IGVFFI2329MKLK](/sequence-files/IGVFFI2329MKLK/), [IGVFFI6615RUKJ](/sequence-files/IGVFFI6615RUKJ/), [IGVFFI5801AZHS](/sequence-files/IGVFFI5801AZHS/), [IGVFFI3077EWVW](/sequence-files/IGVFFI3077EWVW/) 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/IGVFDS8230NTUC/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8230NTUC](/measurement-sets/IGVFDS8230NTUC/) has sequence file(s): [IGVFFI1638QNHU](/sequence-files/IGVFFI1638QNHU/), [IGVFFI8172TTYS](/sequence-files/IGVFFI8172TTYS/), [IGVFFI0061YGQF](/sequence-files/IGVFFI0061YGQF/), [IGVFFI3686ZRQS](/sequence-files/IGVFFI3686ZRQS/), [IGVFFI6949GTER](/sequence-files/IGVFFI6949GTER/), [IGVFFI3279TAQE](/sequence-files/IGVFFI3279TAQE/), [IGVFFI8727IKUM](/sequence-files/IGVFFI8727IKUM/), [IGVFFI7827ZTZF](/sequence-files/IGVFFI7827ZTZF/), [IGVFFI6144MQEY](/sequence-files/IGVFFI6144MQEY/), [IGVFFI4281XRDL](/sequence-files/IGVFFI4281XRDL/), [IGVFFI2270TQZD](/sequence-files/IGVFFI2270TQZD/), [IGVFFI2208XXCI](/sequence-files/IGVFFI2208XXCI/), [IGVFFI5200YQBH](/sequence-files/IGVFFI5200YQBH/), [IGVFFI8366PMMG](/sequence-files/IGVFFI8366PMMG/), [IGVFFI7627ZADE](/sequence-files/IGVFFI7627ZADE/), [IGVFFI6692FXTI](/sequence-files/IGVFFI6692FXTI/), [IGVFFI9001SWZI](/sequence-files/IGVFFI9001SWZI/), [IGVFFI0822KFZB](/sequence-files/IGVFFI0822KFZB/), [IGVFFI0598DIFH](/sequence-files/IGVFFI0598DIFH/), [IGVFFI1052WTYQ](/sequence-files/IGVFFI1052WTYQ/), [IGVFFI9217FRPG](/sequence-files/IGVFFI9217FRPG/), [IGVFFI9341OMBK](/sequence-files/IGVFFI9341OMBK/), [IGVFFI9733FYOF](/sequence-files/IGVFFI9733FYOF/), [IGVFFI6982IYEP](/sequence-files/IGVFFI6982IYEP/), [IGVFFI8307AIRB](/sequence-files/IGVFFI8307AIRB/), [IGVFFI7017LKDP](/sequence-files/IGVFFI7017LKDP/), [IGVFFI0108HSLI](/sequence-files/IGVFFI0108HSLI/), [IGVFFI7081DOTN](/sequence-files/IGVFFI7081DOTN/), [IGVFFI7866CQDH](/sequence-files/IGVFFI7866CQDH/), [IGVFFI6560YHHV](/sequence-files/IGVFFI6560YHHV/), [IGVFFI9378LDZC](/sequence-files/IGVFFI9378LDZC/), [IGVFFI1538CDMZ](/sequence-files/IGVFFI1538CDMZ/), [IGVFFI5728SDMD](/sequence-files/IGVFFI5728SDMD/), [IGVFFI8518JZNQ](/sequence-files/IGVFFI8518JZNQ/), [IGVFFI9741PXPZ](/sequence-files/IGVFFI9741PXPZ/), [IGVFFI7848COEW](/sequence-files/IGVFFI7848COEW/), [IGVFFI7703LMEB](/sequence-files/IGVFFI7703LMEB/), [IGVFFI2462RXKB](/sequence-files/IGVFFI2462RXKB/), [IGVFFI6712QPAZ](/sequence-files/IGVFFI6712QPAZ/), [IGVFFI0296XPVN](/sequence-files/IGVFFI0296XPVN/), [IGVFFI9092XYMC](/sequence-files/IGVFFI9092XYMC/), [IGVFFI0243XBSC](/sequence-files/IGVFFI0243XBSC/), [IGVFFI6371GIAC](/sequence-files/IGVFFI6371GIAC/), [IGVFFI9636RTHI](/sequence-files/IGVFFI9636RTHI/), [IGVFFI2329MKLK](/sequence-files/IGVFFI2329MKLK/), [IGVFFI6615RUKJ](/sequence-files/IGVFFI6615RUKJ/), [IGVFFI5801AZHS](/sequence-files/IGVFFI5801AZHS/), [IGVFFI3077EWVW](/sequence-files/IGVFFI3077EWVW/) 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/IGVFDS8230NTUC/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS8230NTUC](/measurement-sets/IGVFDS8230NTUC/) 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/IGVFDS8230NTUC/"
            }
        ]
    },
    "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": "2024-11-25T23:53:50.386209+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/IGVFFI1638QNHU/",
            "accession": "IGVFFI1638QNHU",
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            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:25:41.829914+00:00",
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            "sequencing_platform": {
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                "term_name": "Illumina NovaSeq X"
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI8172TTYS/",
            "accession": "IGVFFI8172TTYS",
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI0061YGQF/",
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            "content_type": "reads",
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        },
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            "@id": "/sequence-files/IGVFFI3686ZRQS/",
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            "creation_timestamp": "2024-11-26T07:38:55.622030+00:00",
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            },
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        },
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            "@id": "/sequence-files/IGVFFI8727IKUM/",
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            "creation_timestamp": "2024-11-26T07:27:18.747649+00:00",
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        },
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            "@id": "/sequence-files/IGVFFI7827ZTZF/",
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            "upload_status": "validated"
        },
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            ],
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4281XRDL/",
            "accession": "IGVFFI4281XRDL",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinB-PCRrep8_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2024-11-26T07:35:29.716716+00:00",
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            },
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            "upload_status": "validated"
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinB-PCRrep3_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:18:08.705282+00:00",
            "file_format": "fastq",
            "file_size": 6456577,
            "href": "/sequence-files/IGVFFI5801AZHS/@@download/IGVFFI5801AZHS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/24450fe1-55c3-48fc-8761-97e939533344/IGVFFI5801AZHS.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-BinB-PCRrep3_S669_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3077EWVW/",
            "accession": "IGVFFI3077EWVW",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinB-PCRrep5_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:22:44.276783+00:00",
            "file_format": "fastq",
            "file_size": 6479909,
            "href": "/sequence-files/IGVFFI3077EWVW/@@download/IGVFFI3077EWVW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/ba303ddf-3ac8-4857-97c7-f729b7b643c8/IGVFFI3077EWVW.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-BinB-PCRrep5_S671_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/IGVFSM5272HWYP/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5272HWYP",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-BinB"
            ],
            "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 26-50% 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": "2024-11-26T07:25:41.829914+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": "5f2e3340-9181-494f-bcec-97da86bb76d8"
}