IGVFDS8169OPIM

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8169OPIM/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8169OPIM",
    "aliases": [
        "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-BinC_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 [IGVFDS8169OPIM](/measurement-sets/IGVFDS8169OPIM/) has sequence file(s) [IGVFFI4722CNVL](/sequence-files/IGVFFI4722CNVL/), [IGVFFI7431RCGP](/sequence-files/IGVFFI7431RCGP/), [IGVFFI6026BVRJ](/sequence-files/IGVFFI6026BVRJ/), [IGVFFI6476KKYA](/sequence-files/IGVFFI6476KKYA/), [IGVFFI4621AWTZ](/sequence-files/IGVFFI4621AWTZ/), [IGVFFI9512DOCW](/sequence-files/IGVFFI9512DOCW/), [IGVFFI5015ASYV](/sequence-files/IGVFFI5015ASYV/), [IGVFFI7274ZVUO](/sequence-files/IGVFFI7274ZVUO/), [IGVFFI9138RFUI](/sequence-files/IGVFFI9138RFUI/), [IGVFFI0478MTGC](/sequence-files/IGVFFI0478MTGC/), [IGVFFI4926VZKS](/sequence-files/IGVFFI4926VZKS/), [IGVFFI7018SHCD](/sequence-files/IGVFFI7018SHCD/), [IGVFFI5726TPBT](/sequence-files/IGVFFI5726TPBT/), [IGVFFI5351SZWH](/sequence-files/IGVFFI5351SZWH/), [IGVFFI9899BCVQ](/sequence-files/IGVFFI9899BCVQ/), [IGVFFI4069GOTP](/sequence-files/IGVFFI4069GOTP/) 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/IGVFDS8169OPIM/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8169OPIM](/measurement-sets/IGVFDS8169OPIM/) has sequence file(s): [IGVFFI4722CNVL](/sequence-files/IGVFFI4722CNVL/), [IGVFFI7431RCGP](/sequence-files/IGVFFI7431RCGP/), [IGVFFI6026BVRJ](/sequence-files/IGVFFI6026BVRJ/), [IGVFFI6476KKYA](/sequence-files/IGVFFI6476KKYA/), [IGVFFI4621AWTZ](/sequence-files/IGVFFI4621AWTZ/), [IGVFFI9512DOCW](/sequence-files/IGVFFI9512DOCW/), [IGVFFI5015ASYV](/sequence-files/IGVFFI5015ASYV/), [IGVFFI7274ZVUO](/sequence-files/IGVFFI7274ZVUO/), [IGVFFI9138RFUI](/sequence-files/IGVFFI9138RFUI/), [IGVFFI0478MTGC](/sequence-files/IGVFFI0478MTGC/), [IGVFFI4926VZKS](/sequence-files/IGVFFI4926VZKS/), [IGVFFI7018SHCD](/sequence-files/IGVFFI7018SHCD/), [IGVFFI5726TPBT](/sequence-files/IGVFFI5726TPBT/), [IGVFFI5351SZWH](/sequence-files/IGVFFI5351SZWH/), [IGVFFI9899BCVQ](/sequence-files/IGVFFI9899BCVQ/), [IGVFFI4069GOTP](/sequence-files/IGVFFI4069GOTP/) 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/IGVFDS8169OPIM/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS8169OPIM](/measurement-sets/IGVFDS8169OPIM/) 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/IGVFDS8169OPIM/"
            }
        ]
    },
    "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/IGVFDS8210FQOO/",
            "accession": "IGVFDS8210FQOO",
            "aliases": [
                "jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
            ],
            "status": "preview"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-12-10T22:31:48.984029+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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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9899BCVQ/",
            "accession": "IGVFFI9899BCVQ",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-BinC-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T23:26:19.510882+00:00",
            "file_format": "fastq",
            "file_size": 8188978,
            "href": "/sequence-files/IGVFFI9899BCVQ/@@download/IGVFFI9899BCVQ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/378dc7ad-a345-4743-90b1-dbfa07607c9b/IGVFFI9899BCVQ.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinC-PCRrep1_S825_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4069GOTP/",
            "accession": "IGVFFI4069GOTP",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-BinC-PCRrep3_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T23:32:23.978882+00:00",
            "file_format": "fastq",
            "file_size": 5961867,
            "href": "/sequence-files/IGVFFI4069GOTP/@@download/IGVFFI4069GOTP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/c86870be-abc8-4763-8fc3-34b9c95e8fc4/IGVFFI4069GOTP.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinC-PCRrep3_S849_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1132MKHT/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "preferred_assay_title": "Variant-EFFECTS",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4927UHAC/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4927UHAC",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-BinC"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2432IDGC/",
                    "accession": "IGVFDS2432IDGC",
                    "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 51-75% 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": "2024-12-11T00:31:19.214359+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": "34d7e67e-d438-4eca-b717-c9fe2b1f12d8"
}