IGVFDS3851BRIR

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS3851BRIR/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3851BRIR",
    "aliases": [
        "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-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 [IGVFDS3851BRIR](/measurement-sets/IGVFDS3851BRIR/) has sequence file(s) [IGVFFI4681JJQU](/sequence-files/IGVFFI4681JJQU/), [IGVFFI6019KBPU](/sequence-files/IGVFFI6019KBPU/), [IGVFFI9263UIPQ](/sequence-files/IGVFFI9263UIPQ/), [IGVFFI9354LEAI](/sequence-files/IGVFFI9354LEAI/), [IGVFFI4453WUWY](/sequence-files/IGVFFI4453WUWY/), [IGVFFI2031WQUS](/sequence-files/IGVFFI2031WQUS/), [IGVFFI2811LZOB](/sequence-files/IGVFFI2811LZOB/), [IGVFFI5465RPHE](/sequence-files/IGVFFI5465RPHE/), [IGVFFI7555JFRV](/sequence-files/IGVFFI7555JFRV/), [IGVFFI0164SMWZ](/sequence-files/IGVFFI0164SMWZ/), [IGVFFI6394DTCB](/sequence-files/IGVFFI6394DTCB/), [IGVFFI8201TUVA](/sequence-files/IGVFFI8201TUVA/), [IGVFFI3999OLAN](/sequence-files/IGVFFI3999OLAN/), [IGVFFI3898SMKF](/sequence-files/IGVFFI3898SMKF/), [IGVFFI4261ECFC](/sequence-files/IGVFFI4261ECFC/), [IGVFFI0313MOJT](/sequence-files/IGVFFI0313MOJT/), [IGVFFI2531IHCY](/sequence-files/IGVFFI2531IHCY/), [IGVFFI3750LJQP](/sequence-files/IGVFFI3750LJQP/), [IGVFFI2376MHTK](/sequence-files/IGVFFI2376MHTK/), [IGVFFI5196UNTE](/sequence-files/IGVFFI5196UNTE/), [IGVFFI2891YIVE](/sequence-files/IGVFFI2891YIVE/), [IGVFFI8635EGSK](/sequence-files/IGVFFI8635EGSK/), [IGVFFI8591ZVJA](/sequence-files/IGVFFI8591ZVJA/), [IGVFFI6528INGJ](/sequence-files/IGVFFI6528INGJ/), [IGVFFI7436SVLH](/sequence-files/IGVFFI7436SVLH/), [IGVFFI5631RIVN](/sequence-files/IGVFFI5631RIVN/), [IGVFFI3232TPKL](/sequence-files/IGVFFI3232TPKL/), [IGVFFI4267JLLE](/sequence-files/IGVFFI4267JLLE/), [IGVFFI7555TWUS](/sequence-files/IGVFFI7555TWUS/), [IGVFFI0105IKHF](/sequence-files/IGVFFI0105IKHF/), [IGVFFI4975MKQI](/sequence-files/IGVFFI4975MKQI/), [IGVFFI1970PISO](/sequence-files/IGVFFI1970PISO/) 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/IGVFDS3851BRIR/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS3851BRIR](/measurement-sets/IGVFDS3851BRIR/) has sequence file(s): [IGVFFI4681JJQU](/sequence-files/IGVFFI4681JJQU/), [IGVFFI6019KBPU](/sequence-files/IGVFFI6019KBPU/), [IGVFFI9263UIPQ](/sequence-files/IGVFFI9263UIPQ/), [IGVFFI9354LEAI](/sequence-files/IGVFFI9354LEAI/), [IGVFFI4453WUWY](/sequence-files/IGVFFI4453WUWY/), [IGVFFI2031WQUS](/sequence-files/IGVFFI2031WQUS/), [IGVFFI2811LZOB](/sequence-files/IGVFFI2811LZOB/), [IGVFFI5465RPHE](/sequence-files/IGVFFI5465RPHE/), [IGVFFI7555JFRV](/sequence-files/IGVFFI7555JFRV/), [IGVFFI0164SMWZ](/sequence-files/IGVFFI0164SMWZ/), [IGVFFI6394DTCB](/sequence-files/IGVFFI6394DTCB/), [IGVFFI8201TUVA](/sequence-files/IGVFFI8201TUVA/), [IGVFFI3999OLAN](/sequence-files/IGVFFI3999OLAN/), [IGVFFI3898SMKF](/sequence-files/IGVFFI3898SMKF/), [IGVFFI4261ECFC](/sequence-files/IGVFFI4261ECFC/), [IGVFFI0313MOJT](/sequence-files/IGVFFI0313MOJT/), [IGVFFI2531IHCY](/sequence-files/IGVFFI2531IHCY/), [IGVFFI3750LJQP](/sequence-files/IGVFFI3750LJQP/), [IGVFFI2376MHTK](/sequence-files/IGVFFI2376MHTK/), [IGVFFI5196UNTE](/sequence-files/IGVFFI5196UNTE/), [IGVFFI2891YIVE](/sequence-files/IGVFFI2891YIVE/), [IGVFFI8635EGSK](/sequence-files/IGVFFI8635EGSK/), [IGVFFI8591ZVJA](/sequence-files/IGVFFI8591ZVJA/), [IGVFFI6528INGJ](/sequence-files/IGVFFI6528INGJ/), [IGVFFI7436SVLH](/sequence-files/IGVFFI7436SVLH/), [IGVFFI5631RIVN](/sequence-files/IGVFFI5631RIVN/), [IGVFFI3232TPKL](/sequence-files/IGVFFI3232TPKL/), [IGVFFI4267JLLE](/sequence-files/IGVFFI4267JLLE/), [IGVFFI7555TWUS](/sequence-files/IGVFFI7555TWUS/), [IGVFFI0105IKHF](/sequence-files/IGVFFI0105IKHF/), [IGVFFI4975MKQI](/sequence-files/IGVFFI4975MKQI/), [IGVFFI1970PISO](/sequence-files/IGVFFI1970PISO/) 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/IGVFDS3851BRIR/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM8079DJVX](/in-vitro-systems/IGVFSM8079DJVX/) 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/IGVFSM8079DJVX/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM8079DJVX](/in-vitro-systems/IGVFSM8079DJVX/) 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/IGVFSM8079DJVX/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS3851BRIR](/measurement-sets/IGVFDS3851BRIR/) 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/IGVFDS3851BRIR/"
            }
        ]
    },
    "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": "2024-11-22T00:47:29.504703+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": [
        {
            "@id": "/sequence-files/IGVFFI4681JJQU/",
            "accession": "IGVFFI4681JJQU",
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            "creation_timestamp": "2024-11-22T05:54:17.051081+00:00",
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            },
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI6019KBPU/",
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        },
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        "title": "Jesse Engreitz, Stanford"
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    "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/IGVFSM8079DJVX/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8079DJVX",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep2-BinC"
            ],
            "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 51-75% 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": "2024-11-22T05:48:26.388536+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": "c0fad0f9-ca8f-4775-aecd-d2d55688b050"
}