IGVFDS2226SPYF

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS2226SPYF/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2226SPYF",
    "aliases": [
        "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinD_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 [IGVFDS2226SPYF](/measurement-sets/IGVFDS2226SPYF/) has sequence file(s) [IGVFFI0626BGLQ](/sequence-files/IGVFFI0626BGLQ/), [IGVFFI8681AYRN](/sequence-files/IGVFFI8681AYRN/), [IGVFFI9027IUEG](/sequence-files/IGVFFI9027IUEG/), [IGVFFI8420QXDT](/sequence-files/IGVFFI8420QXDT/), [IGVFFI1266XPEQ](/sequence-files/IGVFFI1266XPEQ/), [IGVFFI6008XUPU](/sequence-files/IGVFFI6008XUPU/), [IGVFFI2151BDTN](/sequence-files/IGVFFI2151BDTN/), [IGVFFI8910RYPU](/sequence-files/IGVFFI8910RYPU/), [IGVFFI1795MDAU](/sequence-files/IGVFFI1795MDAU/), [IGVFFI3674KVZX](/sequence-files/IGVFFI3674KVZX/), [IGVFFI2881JQQB](/sequence-files/IGVFFI2881JQQB/), [IGVFFI3129HQXY](/sequence-files/IGVFFI3129HQXY/), [IGVFFI4696UXEU](/sequence-files/IGVFFI4696UXEU/), [IGVFFI2269HMLY](/sequence-files/IGVFFI2269HMLY/), [IGVFFI4618GSXT](/sequence-files/IGVFFI4618GSXT/), [IGVFFI3347LXMJ](/sequence-files/IGVFFI3347LXMJ/), [IGVFFI6837WCJX](/sequence-files/IGVFFI6837WCJX/), [IGVFFI3821BRQS](/sequence-files/IGVFFI3821BRQS/), [IGVFFI0268YQSF](/sequence-files/IGVFFI0268YQSF/), [IGVFFI9249UUWF](/sequence-files/IGVFFI9249UUWF/), [IGVFFI4978DUYW](/sequence-files/IGVFFI4978DUYW/), [IGVFFI8445YYFS](/sequence-files/IGVFFI8445YYFS/), [IGVFFI8662ICZA](/sequence-files/IGVFFI8662ICZA/), [IGVFFI6338CHKJ](/sequence-files/IGVFFI6338CHKJ/), [IGVFFI0229FWHC](/sequence-files/IGVFFI0229FWHC/), [IGVFFI3619ZVHW](/sequence-files/IGVFFI3619ZVHW/), [IGVFFI7553VASE](/sequence-files/IGVFFI7553VASE/), [IGVFFI7636QZXT](/sequence-files/IGVFFI7636QZXT/), [IGVFFI1839KWJP](/sequence-files/IGVFFI1839KWJP/), [IGVFFI8427EAFE](/sequence-files/IGVFFI8427EAFE/), [IGVFFI3062JPOB](/sequence-files/IGVFFI3062JPOB/), [IGVFFI5773UCDZ](/sequence-files/IGVFFI5773UCDZ/) 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/IGVFDS2226SPYF/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS2226SPYF](/measurement-sets/IGVFDS2226SPYF/) has sequence file(s): [IGVFFI0626BGLQ](/sequence-files/IGVFFI0626BGLQ/), [IGVFFI8681AYRN](/sequence-files/IGVFFI8681AYRN/), [IGVFFI9027IUEG](/sequence-files/IGVFFI9027IUEG/), [IGVFFI8420QXDT](/sequence-files/IGVFFI8420QXDT/), [IGVFFI1266XPEQ](/sequence-files/IGVFFI1266XPEQ/), [IGVFFI6008XUPU](/sequence-files/IGVFFI6008XUPU/), [IGVFFI2151BDTN](/sequence-files/IGVFFI2151BDTN/), [IGVFFI8910RYPU](/sequence-files/IGVFFI8910RYPU/), [IGVFFI1795MDAU](/sequence-files/IGVFFI1795MDAU/), [IGVFFI3674KVZX](/sequence-files/IGVFFI3674KVZX/), [IGVFFI2881JQQB](/sequence-files/IGVFFI2881JQQB/), [IGVFFI3129HQXY](/sequence-files/IGVFFI3129HQXY/), [IGVFFI4696UXEU](/sequence-files/IGVFFI4696UXEU/), [IGVFFI2269HMLY](/sequence-files/IGVFFI2269HMLY/), [IGVFFI4618GSXT](/sequence-files/IGVFFI4618GSXT/), [IGVFFI3347LXMJ](/sequence-files/IGVFFI3347LXMJ/), [IGVFFI6837WCJX](/sequence-files/IGVFFI6837WCJX/), [IGVFFI3821BRQS](/sequence-files/IGVFFI3821BRQS/), [IGVFFI0268YQSF](/sequence-files/IGVFFI0268YQSF/), [IGVFFI9249UUWF](/sequence-files/IGVFFI9249UUWF/), [IGVFFI4978DUYW](/sequence-files/IGVFFI4978DUYW/), [IGVFFI8445YYFS](/sequence-files/IGVFFI8445YYFS/), [IGVFFI8662ICZA](/sequence-files/IGVFFI8662ICZA/), [IGVFFI6338CHKJ](/sequence-files/IGVFFI6338CHKJ/), [IGVFFI0229FWHC](/sequence-files/IGVFFI0229FWHC/), [IGVFFI3619ZVHW](/sequence-files/IGVFFI3619ZVHW/), [IGVFFI7553VASE](/sequence-files/IGVFFI7553VASE/), [IGVFFI7636QZXT](/sequence-files/IGVFFI7636QZXT/), [IGVFFI1839KWJP](/sequence-files/IGVFFI1839KWJP/), [IGVFFI8427EAFE](/sequence-files/IGVFFI8427EAFE/), [IGVFFI3062JPOB](/sequence-files/IGVFFI3062JPOB/), [IGVFFI5773UCDZ](/sequence-files/IGVFFI5773UCDZ/) 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/IGVFDS2226SPYF/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM5709XAIS](/in-vitro-systems/IGVFSM5709XAIS/) 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/IGVFSM5709XAIS/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM5709XAIS](/in-vitro-systems/IGVFSM5709XAIS/) 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/IGVFSM5709XAIS/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS2226SPYF](/measurement-sets/IGVFDS2226SPYF/) 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/IGVFDS2226SPYF/"
            }
        ]
    },
    "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": "2024-11-22T00:47:58.990173+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/IGVFFI0626BGLQ/",
            "accession": "IGVFFI0626BGLQ",
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            "creation_timestamp": "2024-11-22T06:08:02.616747+00:00",
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                "term_name": "Illumina NovaSeq X"
            },
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            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-PCRRep3-BinD_S60_R1_001.fastq.gz",
            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI8681AYRN/",
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI9027IUEG/",
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        },
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            "@id": "/sequence-files/IGVFFI8420QXDT/",
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        },
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        },
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            "@id": "/sequence-files/IGVFFI2151BDTN/",
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        },
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            "@id": "/sequence-files/IGVFFI1795MDAU/",
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        },
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        },
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            "@id": "/sequence-files/IGVFFI3129HQXY/",
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            "upload_status": "validated"
        },
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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/IGVFSM5709XAIS/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM5709XAIS",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep1-FFRep3-BinD"
            ],
            "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 76-100% 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": "2024-11-22T06:04:11.654750+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": "e99c0c89-03a0-4772-b353-41f5a006d712"
}