IGVFDS3465JQXG

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS3465JQXG/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3465JQXG",
    "aliases": [
        "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input_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 [IGVFDS3465JQXG](/measurement-sets/IGVFDS3465JQXG/) has sequence file(s) [IGVFFI7856CVGD](/sequence-files/IGVFFI7856CVGD/), [IGVFFI2364MYCD](/sequence-files/IGVFFI2364MYCD/), [IGVFFI1009QSPW](/sequence-files/IGVFFI1009QSPW/), [IGVFFI6125LNYA](/sequence-files/IGVFFI6125LNYA/), [IGVFFI1073ATRZ](/sequence-files/IGVFFI1073ATRZ/), [IGVFFI0219BOCG](/sequence-files/IGVFFI0219BOCG/), [IGVFFI0839MJWJ](/sequence-files/IGVFFI0839MJWJ/), [IGVFFI4770UACM](/sequence-files/IGVFFI4770UACM/) 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/IGVFDS3465JQXG/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS3465JQXG](/measurement-sets/IGVFDS3465JQXG/) has sequence file(s): [IGVFFI7856CVGD](/sequence-files/IGVFFI7856CVGD/), [IGVFFI2364MYCD](/sequence-files/IGVFFI2364MYCD/), [IGVFFI1009QSPW](/sequence-files/IGVFFI1009QSPW/), [IGVFFI6125LNYA](/sequence-files/IGVFFI6125LNYA/), [IGVFFI1073ATRZ](/sequence-files/IGVFFI1073ATRZ/), [IGVFFI0219BOCG](/sequence-files/IGVFFI0219BOCG/), [IGVFFI0839MJWJ](/sequence-files/IGVFFI0839MJWJ/), [IGVFFI4770UACM](/sequence-files/IGVFFI4770UACM/) 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/IGVFDS3465JQXG/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS3465JQXG](/measurement-sets/IGVFDS3465JQXG/) 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/IGVFDS3465JQXG/"
            }
        ]
    },
    "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": "2024-12-10T22:33:19.749898+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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                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T00:54:37.059566+00:00",
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            "file_size": 45290194,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2364MYCD/",
            "accession": "IGVFFI2364MYCD",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T00:57:34.084628+00:00",
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            "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-BioRep2-FFrep1-BinAll-PCRrep2_S985_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1009QSPW/",
            "accession": "IGVFFI1009QSPW",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T19:25:03.828575+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S973_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6125LNYA/",
            "accession": "IGVFFI6125LNYA",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T19:28:13.736253+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S985_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1073ATRZ/",
            "accession": "IGVFFI1073ATRZ",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T21:36:57.958225+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0219BOCG/",
            "accession": "IGVFFI0219BOCG",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T23:53:05.733173+00:00",
            "file_format": "fastq",
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S985_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0839MJWJ/",
            "accession": "IGVFFI0839MJWJ",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T21:40:10.925610+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep2_S985_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4770UACM/",
            "accession": "IGVFFI4770UACM",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T23:49:57.931387+00:00",
            "file_format": "fastq",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep2-FFrep1-BinAll-PCRrep1_S973_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/IGVFSM0397MOBU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0397MOBU",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep2-FFrep1-FACS_Input"
            ],
            "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 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": "2024-12-11T00:54:37.059566+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": "65775dda-d8f8-4a29-8735-36e0f8fee470"
}