IGVFDS7723OVPC

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7723OVPC/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7723OVPC",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinA_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 [IGVFDS7723OVPC](/measurement-sets/IGVFDS7723OVPC/) has sequence file(s) [IGVFFI9191BBXD](/sequence-files/IGVFFI9191BBXD/), [IGVFFI5281TEWH](/sequence-files/IGVFFI5281TEWH/), [IGVFFI1289IQYL](/sequence-files/IGVFFI1289IQYL/), [IGVFFI8456SULG](/sequence-files/IGVFFI8456SULG/), [IGVFFI6690NIDX](/sequence-files/IGVFFI6690NIDX/), [IGVFFI4680LHLH](/sequence-files/IGVFFI4680LHLH/), [IGVFFI0571KMZO](/sequence-files/IGVFFI0571KMZO/), [IGVFFI1880WCRB](/sequence-files/IGVFFI1880WCRB/), [IGVFFI6607WXEB](/sequence-files/IGVFFI6607WXEB/), [IGVFFI8840WSRI](/sequence-files/IGVFFI8840WSRI/), [IGVFFI5515FNHI](/sequence-files/IGVFFI5515FNHI/), [IGVFFI9026SAGO](/sequence-files/IGVFFI9026SAGO/), [IGVFFI0583HHIS](/sequence-files/IGVFFI0583HHIS/), [IGVFFI3734XORT](/sequence-files/IGVFFI3734XORT/), [IGVFFI7085EEEO](/sequence-files/IGVFFI7085EEEO/), [IGVFFI1161GSIX](/sequence-files/IGVFFI1161GSIX/), [IGVFFI8690SKUA](/sequence-files/IGVFFI8690SKUA/), [IGVFFI4834EPJD](/sequence-files/IGVFFI4834EPJD/), [IGVFFI5596QPHW](/sequence-files/IGVFFI5596QPHW/), [IGVFFI3934FKCL](/sequence-files/IGVFFI3934FKCL/), [IGVFFI5711FFND](/sequence-files/IGVFFI5711FFND/), [IGVFFI6429KCWE](/sequence-files/IGVFFI6429KCWE/), [IGVFFI3126NYAW](/sequence-files/IGVFFI3126NYAW/), [IGVFFI9587TGGB](/sequence-files/IGVFFI9587TGGB/), [IGVFFI9882GZNO](/sequence-files/IGVFFI9882GZNO/), [IGVFFI1415OSPP](/sequence-files/IGVFFI1415OSPP/), [IGVFFI0780SOMN](/sequence-files/IGVFFI0780SOMN/), [IGVFFI3095RSYS](/sequence-files/IGVFFI3095RSYS/), [IGVFFI4446YVOU](/sequence-files/IGVFFI4446YVOU/), [IGVFFI2884VMCZ](/sequence-files/IGVFFI2884VMCZ/), [IGVFFI5713INXZ](/sequence-files/IGVFFI5713INXZ/), [IGVFFI7317VIWQ](/sequence-files/IGVFFI7317VIWQ/), [IGVFFI5435NDLP](/sequence-files/IGVFFI5435NDLP/), [IGVFFI5932XSTE](/sequence-files/IGVFFI5932XSTE/), [IGVFFI7651WNFO](/sequence-files/IGVFFI7651WNFO/), [IGVFFI7767OIZP](/sequence-files/IGVFFI7767OIZP/), [IGVFFI1853JQBW](/sequence-files/IGVFFI1853JQBW/), [IGVFFI9177AXZK](/sequence-files/IGVFFI9177AXZK/), [IGVFFI7645QXJK](/sequence-files/IGVFFI7645QXJK/), [IGVFFI9758GKVN](/sequence-files/IGVFFI9758GKVN/), [IGVFFI4345GCVY](/sequence-files/IGVFFI4345GCVY/), [IGVFFI6511SUIM](/sequence-files/IGVFFI6511SUIM/), [IGVFFI2313UKWW](/sequence-files/IGVFFI2313UKWW/), [IGVFFI0639FMWJ](/sequence-files/IGVFFI0639FMWJ/), [IGVFFI6563XSLJ](/sequence-files/IGVFFI6563XSLJ/), [IGVFFI7228DLQD](/sequence-files/IGVFFI7228DLQD/), [IGVFFI9582RTKF](/sequence-files/IGVFFI9582RTKF/), [IGVFFI8653TJFI](/sequence-files/IGVFFI8653TJFI/) 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/IGVFDS7723OVPC/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7723OVPC](/measurement-sets/IGVFDS7723OVPC/) has sequence file(s): [IGVFFI9191BBXD](/sequence-files/IGVFFI9191BBXD/), [IGVFFI5281TEWH](/sequence-files/IGVFFI5281TEWH/), [IGVFFI1289IQYL](/sequence-files/IGVFFI1289IQYL/), [IGVFFI8456SULG](/sequence-files/IGVFFI8456SULG/), [IGVFFI6690NIDX](/sequence-files/IGVFFI6690NIDX/), [IGVFFI4680LHLH](/sequence-files/IGVFFI4680LHLH/), [IGVFFI0571KMZO](/sequence-files/IGVFFI0571KMZO/), [IGVFFI1880WCRB](/sequence-files/IGVFFI1880WCRB/), [IGVFFI6607WXEB](/sequence-files/IGVFFI6607WXEB/), [IGVFFI8840WSRI](/sequence-files/IGVFFI8840WSRI/), [IGVFFI5515FNHI](/sequence-files/IGVFFI5515FNHI/), [IGVFFI9026SAGO](/sequence-files/IGVFFI9026SAGO/), [IGVFFI0583HHIS](/sequence-files/IGVFFI0583HHIS/), [IGVFFI3734XORT](/sequence-files/IGVFFI3734XORT/), [IGVFFI7085EEEO](/sequence-files/IGVFFI7085EEEO/), [IGVFFI1161GSIX](/sequence-files/IGVFFI1161GSIX/), [IGVFFI8690SKUA](/sequence-files/IGVFFI8690SKUA/), [IGVFFI4834EPJD](/sequence-files/IGVFFI4834EPJD/), [IGVFFI5596QPHW](/sequence-files/IGVFFI5596QPHW/), [IGVFFI3934FKCL](/sequence-files/IGVFFI3934FKCL/), [IGVFFI5711FFND](/sequence-files/IGVFFI5711FFND/), [IGVFFI6429KCWE](/sequence-files/IGVFFI6429KCWE/), [IGVFFI3126NYAW](/sequence-files/IGVFFI3126NYAW/), [IGVFFI9587TGGB](/sequence-files/IGVFFI9587TGGB/), [IGVFFI9882GZNO](/sequence-files/IGVFFI9882GZNO/), [IGVFFI1415OSPP](/sequence-files/IGVFFI1415OSPP/), [IGVFFI0780SOMN](/sequence-files/IGVFFI0780SOMN/), [IGVFFI3095RSYS](/sequence-files/IGVFFI3095RSYS/), [IGVFFI4446YVOU](/sequence-files/IGVFFI4446YVOU/), [IGVFFI2884VMCZ](/sequence-files/IGVFFI2884VMCZ/), [IGVFFI5713INXZ](/sequence-files/IGVFFI5713INXZ/), [IGVFFI7317VIWQ](/sequence-files/IGVFFI7317VIWQ/), [IGVFFI5435NDLP](/sequence-files/IGVFFI5435NDLP/), [IGVFFI5932XSTE](/sequence-files/IGVFFI5932XSTE/), [IGVFFI7651WNFO](/sequence-files/IGVFFI7651WNFO/), [IGVFFI7767OIZP](/sequence-files/IGVFFI7767OIZP/), [IGVFFI1853JQBW](/sequence-files/IGVFFI1853JQBW/), [IGVFFI9177AXZK](/sequence-files/IGVFFI9177AXZK/), [IGVFFI7645QXJK](/sequence-files/IGVFFI7645QXJK/), [IGVFFI9758GKVN](/sequence-files/IGVFFI9758GKVN/), [IGVFFI4345GCVY](/sequence-files/IGVFFI4345GCVY/), [IGVFFI6511SUIM](/sequence-files/IGVFFI6511SUIM/), [IGVFFI2313UKWW](/sequence-files/IGVFFI2313UKWW/), [IGVFFI0639FMWJ](/sequence-files/IGVFFI0639FMWJ/), [IGVFFI6563XSLJ](/sequence-files/IGVFFI6563XSLJ/), [IGVFFI7228DLQD](/sequence-files/IGVFFI7228DLQD/), [IGVFFI9582RTKF](/sequence-files/IGVFFI9582RTKF/), [IGVFFI8653TJFI](/sequence-files/IGVFFI8653TJFI/) 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/IGVFDS7723OVPC/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7723OVPC](/measurement-sets/IGVFDS7723OVPC/) 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/IGVFDS7723OVPC/"
            }
        ]
    },
    "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": "2024-11-25T23:54:29.679478+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/IGVFFI9191BBXD/",
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            "content_type": "reads",
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        },
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        },
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            "aliases": [
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            ],
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        },
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep6_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:23:16.874493+00:00",
            "file_format": "fastq",
            "file_size": 6711057,
            "href": "/sequence-files/IGVFFI9582RTKF/@@download/IGVFFI9582RTKF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/86943cd8-3a5d-4bcd-a3df-38517d6270ba/IGVFFI9582RTKF.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-BinA-PCRrep6_S756_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8653TJFI/",
            "accession": "IGVFFI8653TJFI",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinA-PCRrep11_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:35:10.796238+00:00",
            "file_format": "fastq",
            "file_size": 6185238,
            "href": "/sequence-files/IGVFFI8653TJFI/@@download/IGVFFI8653TJFI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/674cf3e6-51db-4dd6-981a-d2b7956ae8da/IGVFFI8653TJFI.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-BinA-PCRrep11_S761_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/IGVFSM9601DQGW/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9601DQGW",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-BinA"
            ],
            "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 0-25% 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": "2024-11-26T07:56:23.146035+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": "e38fe8f1-a020-44d0-8cfa-5340b8eb5bbf"
}