IGVFDS2408JJSR

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2408JJSR/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2408JJSR",
    "aliases": [
        "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-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": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM7352WPEI](/in-vitro-systems/IGVFSM7352WPEI/) has in progress subobject treatment [cf87f410-54ee-48ef-b654-8443c4fee032](/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM7352WPEI/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM7352WPEI](/in-vitro-systems/IGVFSM7352WPEI/) has in progress subobject treatment [4b5f0d13-ec20-4b91-85f5-a009cd91451f](/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM7352WPEI/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS2408JJSR](/measurement-sets/IGVFDS2408JJSR/) has sequence file(s) [IGVFFI9077WPOS](/sequence-files/IGVFFI9077WPOS/), [IGVFFI4302VEKL](/sequence-files/IGVFFI4302VEKL/), [IGVFFI2917ZNGJ](/sequence-files/IGVFFI2917ZNGJ/), [IGVFFI4502BFMI](/sequence-files/IGVFFI4502BFMI/), [IGVFFI4508DIPO](/sequence-files/IGVFFI4508DIPO/), [IGVFFI1847PPED](/sequence-files/IGVFFI1847PPED/), [IGVFFI3421MZSL](/sequence-files/IGVFFI3421MZSL/), [IGVFFI5855IABX](/sequence-files/IGVFFI5855IABX/), [IGVFFI0262QWKE](/sequence-files/IGVFFI0262QWKE/), [IGVFFI4394CMYG](/sequence-files/IGVFFI4394CMYG/), [IGVFFI5849NFJR](/sequence-files/IGVFFI5849NFJR/), [IGVFFI6391DPNG](/sequence-files/IGVFFI6391DPNG/), [IGVFFI8266UMNF](/sequence-files/IGVFFI8266UMNF/), [IGVFFI4203TDPR](/sequence-files/IGVFFI4203TDPR/), [IGVFFI7226GFNQ](/sequence-files/IGVFFI7226GFNQ/), [IGVFFI8698MDJX](/sequence-files/IGVFFI8698MDJX/), [IGVFFI2701ZGIQ](/sequence-files/IGVFFI2701ZGIQ/), [IGVFFI7482BEAW](/sequence-files/IGVFFI7482BEAW/), [IGVFFI8840HOED](/sequence-files/IGVFFI8840HOED/), [IGVFFI4319FJLW](/sequence-files/IGVFFI4319FJLW/), [IGVFFI4993MNWD](/sequence-files/IGVFFI4993MNWD/), [IGVFFI2097EXRE](/sequence-files/IGVFFI2097EXRE/), [IGVFFI5273NUWG](/sequence-files/IGVFFI5273NUWG/), [IGVFFI8168GBMR](/sequence-files/IGVFFI8168GBMR/), [IGVFFI0220FXEN](/sequence-files/IGVFFI0220FXEN/), [IGVFFI1814WWXW](/sequence-files/IGVFFI1814WWXW/), [IGVFFI2845WUPP](/sequence-files/IGVFFI2845WUPP/), [IGVFFI4704VLBI](/sequence-files/IGVFFI4704VLBI/), [IGVFFI1067ZSDR](/sequence-files/IGVFFI1067ZSDR/), [IGVFFI4874MIQN](/sequence-files/IGVFFI4874MIQN/), [IGVFFI7649LTWL](/sequence-files/IGVFFI7649LTWL/), [IGVFFI2183ONZB](/sequence-files/IGVFFI2183ONZB/) 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/IGVFDS2408JJSR/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2408JJSR](/measurement-sets/IGVFDS2408JJSR/) has sequence file(s): [IGVFFI9077WPOS](/sequence-files/IGVFFI9077WPOS/), [IGVFFI4302VEKL](/sequence-files/IGVFFI4302VEKL/), [IGVFFI2917ZNGJ](/sequence-files/IGVFFI2917ZNGJ/), [IGVFFI4502BFMI](/sequence-files/IGVFFI4502BFMI/), [IGVFFI4508DIPO](/sequence-files/IGVFFI4508DIPO/), [IGVFFI1847PPED](/sequence-files/IGVFFI1847PPED/), [IGVFFI3421MZSL](/sequence-files/IGVFFI3421MZSL/), [IGVFFI5855IABX](/sequence-files/IGVFFI5855IABX/), [IGVFFI0262QWKE](/sequence-files/IGVFFI0262QWKE/), [IGVFFI4394CMYG](/sequence-files/IGVFFI4394CMYG/), [IGVFFI5849NFJR](/sequence-files/IGVFFI5849NFJR/), [IGVFFI6391DPNG](/sequence-files/IGVFFI6391DPNG/), [IGVFFI8266UMNF](/sequence-files/IGVFFI8266UMNF/), [IGVFFI4203TDPR](/sequence-files/IGVFFI4203TDPR/), [IGVFFI7226GFNQ](/sequence-files/IGVFFI7226GFNQ/), [IGVFFI8698MDJX](/sequence-files/IGVFFI8698MDJX/), [IGVFFI2701ZGIQ](/sequence-files/IGVFFI2701ZGIQ/), [IGVFFI7482BEAW](/sequence-files/IGVFFI7482BEAW/), [IGVFFI8840HOED](/sequence-files/IGVFFI8840HOED/), [IGVFFI4319FJLW](/sequence-files/IGVFFI4319FJLW/), [IGVFFI4993MNWD](/sequence-files/IGVFFI4993MNWD/), [IGVFFI2097EXRE](/sequence-files/IGVFFI2097EXRE/), [IGVFFI5273NUWG](/sequence-files/IGVFFI5273NUWG/), [IGVFFI8168GBMR](/sequence-files/IGVFFI8168GBMR/), [IGVFFI0220FXEN](/sequence-files/IGVFFI0220FXEN/), [IGVFFI1814WWXW](/sequence-files/IGVFFI1814WWXW/), [IGVFFI2845WUPP](/sequence-files/IGVFFI2845WUPP/), [IGVFFI4704VLBI](/sequence-files/IGVFFI4704VLBI/), [IGVFFI1067ZSDR](/sequence-files/IGVFFI1067ZSDR/), [IGVFFI4874MIQN](/sequence-files/IGVFFI4874MIQN/), [IGVFFI7649LTWL](/sequence-files/IGVFFI7649LTWL/), [IGVFFI2183ONZB](/sequence-files/IGVFFI2183ONZB/) 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/IGVFDS2408JJSR/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS2408JJSR](/measurement-sets/IGVFDS2408JJSR/) 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/IGVFDS2408JJSR/"
            }
        ]
    },
    "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/IGVFDS6874YIXA/",
            "accession": "IGVFDS6874YIXA",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-NegControl_AmpliconSequencing"
            ],
            "status": "preview"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-11-22T00:47:23.842004+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1080XFGV/",
            "accession": "IGVFDO1080XFGV",
            "aliases": [
                "igvf:donor_of_Jurkat"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
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            "@id": "/sequence-files/IGVFFI9077WPOS/",
            "accession": "IGVFFI9077WPOS",
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                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinB-PCRRep8_R1"
            ],
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-PCRRep8-BinB_S174_R1_001.fastq.gz",
            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI4302VEKL/",
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            "content_type": "reads",
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        },
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            "@id": "/sequence-files/IGVFFI2917ZNGJ/",
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        },
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            "@id": "/sequence-files/IGVFFI4502BFMI/",
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        },
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            "@id": "/sequence-files/IGVFFI4508DIPO/",
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        },
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        },
        {
            "@id": "/sequence-files/IGVFFI3421MZSL/",
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            ],
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            },
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        },
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        },
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        },
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            "@id": "/sequence-files/IGVFFI4394CMYG/",
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                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinB-PCRRep7_R2"
            ],
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        },
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        },
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            "@id": "/sequence-files/IGVFFI6391DPNG/",
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            "aliases": [
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            ],
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8266UMNF/",
            "accession": "IGVFFI8266UMNF",
            "aliases": [
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            ],
            "content_type": "reads",
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    "preferred_assay_title": "Variant-EFFECTS",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7352WPEI/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7352WPEI",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinB"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6128KVUP/",
                    "accession": "IGVFDS6128KVUP",
                    "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_0002796/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:Jurkat"
                    ],
                    "status": "released",
                    "summary": "Jurkat",
                    "term_name": "Jurkat"
                }
            ],
            "status": "preview",
            "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 26-50% expression of IL2RA) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 24 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 24 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/4b5f0d13-ec20-4b91-85f5-a009cd91451f/",
                    "status": "in progress",
                    "treatment_term_name": "phorbol 13-acetate 12-myristate"
                },
                {
                    "@id": "/treatments/cf87f410-54ee-48ef-b654-8443c4fee032/",
                    "status": "in progress",
                    "treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
                }
            ]
        }
    ],
    "schema_version": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2024-11-22T05:47:55.858326+00:00",
    "summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000134460/",
            "geneid": "ENSG00000134460",
            "name": "interleukin 2 receptor subunit alpha",
            "status": "released",
            "symbol": "IL2RA",
            "synonyms": [
                "interleukin-2 receptor subunit alpha",
                "IL2R",
                "TAC antigen",
                "IMD41",
                "IL-2R subunit alpha",
                "CD25",
                "IL-2 receptor subunit alpha",
                "IDDM10",
                "TCGFR",
                "p55",
                "interleukin 2 receptor, alpha"
            ]
        }
    ],
    "uuid": "6efead97-79fd-4dbf-821e-095291e63af4"
}