IGVFDS9743TYOT

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS9743TYOT/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9743TYOT",
    "aliases": [
        "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-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 [IGVFSM1469NQHM](/in-vitro-systems/IGVFSM1469NQHM/) 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/IGVFSM1469NQHM/"
            },
            {
                "category": "mismatched status",
                "detail": "Preview in vitro system [IGVFSM1469NQHM](/in-vitro-systems/IGVFSM1469NQHM/) 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/IGVFSM1469NQHM/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS9743TYOT](/measurement-sets/IGVFDS9743TYOT/) has sequence file(s) [IGVFFI4079JILX](/sequence-files/IGVFFI4079JILX/), [IGVFFI1373KUKR](/sequence-files/IGVFFI1373KUKR/), [IGVFFI4004OCJK](/sequence-files/IGVFFI4004OCJK/), [IGVFFI5438YNQO](/sequence-files/IGVFFI5438YNQO/), [IGVFFI6623WDMM](/sequence-files/IGVFFI6623WDMM/), [IGVFFI9003OVDO](/sequence-files/IGVFFI9003OVDO/), [IGVFFI6431LCJA](/sequence-files/IGVFFI6431LCJA/), [IGVFFI2836PSYE](/sequence-files/IGVFFI2836PSYE/), [IGVFFI9659HSEI](/sequence-files/IGVFFI9659HSEI/), [IGVFFI2980IPAV](/sequence-files/IGVFFI2980IPAV/), [IGVFFI7719FMIO](/sequence-files/IGVFFI7719FMIO/), [IGVFFI0216UNBO](/sequence-files/IGVFFI0216UNBO/), [IGVFFI0284EXJD](/sequence-files/IGVFFI0284EXJD/), [IGVFFI4763QAAY](/sequence-files/IGVFFI4763QAAY/), [IGVFFI1201EWXS](/sequence-files/IGVFFI1201EWXS/), [IGVFFI4840JNEW](/sequence-files/IGVFFI4840JNEW/), [IGVFFI4837ZJSA](/sequence-files/IGVFFI4837ZJSA/), [IGVFFI3522ZFSE](/sequence-files/IGVFFI3522ZFSE/), [IGVFFI4136UUTG](/sequence-files/IGVFFI4136UUTG/), [IGVFFI3850NQMD](/sequence-files/IGVFFI3850NQMD/), [IGVFFI2947EOWS](/sequence-files/IGVFFI2947EOWS/), [IGVFFI0242KBIS](/sequence-files/IGVFFI0242KBIS/), [IGVFFI4668QMNR](/sequence-files/IGVFFI4668QMNR/), [IGVFFI6260AZKX](/sequence-files/IGVFFI6260AZKX/), [IGVFFI2651LPUP](/sequence-files/IGVFFI2651LPUP/), [IGVFFI2398VVPH](/sequence-files/IGVFFI2398VVPH/), [IGVFFI8969QEUS](/sequence-files/IGVFFI8969QEUS/), [IGVFFI8000RXPO](/sequence-files/IGVFFI8000RXPO/), [IGVFFI6862TNMK](/sequence-files/IGVFFI6862TNMK/), [IGVFFI1739PUZS](/sequence-files/IGVFFI1739PUZS/), [IGVFFI4665JGTL](/sequence-files/IGVFFI4665JGTL/), [IGVFFI2556JBWG](/sequence-files/IGVFFI2556JBWG/) 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/IGVFDS9743TYOT/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS9743TYOT](/measurement-sets/IGVFDS9743TYOT/) has sequence file(s): [IGVFFI4079JILX](/sequence-files/IGVFFI4079JILX/), [IGVFFI1373KUKR](/sequence-files/IGVFFI1373KUKR/), [IGVFFI4004OCJK](/sequence-files/IGVFFI4004OCJK/), [IGVFFI5438YNQO](/sequence-files/IGVFFI5438YNQO/), [IGVFFI6623WDMM](/sequence-files/IGVFFI6623WDMM/), [IGVFFI9003OVDO](/sequence-files/IGVFFI9003OVDO/), [IGVFFI6431LCJA](/sequence-files/IGVFFI6431LCJA/), [IGVFFI2836PSYE](/sequence-files/IGVFFI2836PSYE/), [IGVFFI9659HSEI](/sequence-files/IGVFFI9659HSEI/), [IGVFFI2980IPAV](/sequence-files/IGVFFI2980IPAV/), [IGVFFI7719FMIO](/sequence-files/IGVFFI7719FMIO/), [IGVFFI0216UNBO](/sequence-files/IGVFFI0216UNBO/), [IGVFFI0284EXJD](/sequence-files/IGVFFI0284EXJD/), [IGVFFI4763QAAY](/sequence-files/IGVFFI4763QAAY/), [IGVFFI1201EWXS](/sequence-files/IGVFFI1201EWXS/), [IGVFFI4840JNEW](/sequence-files/IGVFFI4840JNEW/), [IGVFFI4837ZJSA](/sequence-files/IGVFFI4837ZJSA/), [IGVFFI3522ZFSE](/sequence-files/IGVFFI3522ZFSE/), [IGVFFI4136UUTG](/sequence-files/IGVFFI4136UUTG/), [IGVFFI3850NQMD](/sequence-files/IGVFFI3850NQMD/), [IGVFFI2947EOWS](/sequence-files/IGVFFI2947EOWS/), [IGVFFI0242KBIS](/sequence-files/IGVFFI0242KBIS/), [IGVFFI4668QMNR](/sequence-files/IGVFFI4668QMNR/), [IGVFFI6260AZKX](/sequence-files/IGVFFI6260AZKX/), [IGVFFI2651LPUP](/sequence-files/IGVFFI2651LPUP/), [IGVFFI2398VVPH](/sequence-files/IGVFFI2398VVPH/), [IGVFFI8969QEUS](/sequence-files/IGVFFI8969QEUS/), [IGVFFI8000RXPO](/sequence-files/IGVFFI8000RXPO/), [IGVFFI6862TNMK](/sequence-files/IGVFFI6862TNMK/), [IGVFFI1739PUZS](/sequence-files/IGVFFI1739PUZS/), [IGVFFI4665JGTL](/sequence-files/IGVFFI4665JGTL/), [IGVFFI2556JBWG](/sequence-files/IGVFFI2556JBWG/) 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/IGVFDS9743TYOT/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS9743TYOT](/measurement-sets/IGVFDS9743TYOT/) 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/IGVFDS9743TYOT/"
            }
        ]
    },
    "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": "2024-11-22T00:48:13.693664+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/IGVFFI4079JILX/",
            "accession": "IGVFFI4079JILX",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep7_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-22T06:31:03.642958+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": "Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-PCRRep7-BinB_S158_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1373KUKR/",
            "accession": "IGVFFI1373KUKR",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-22T06:20:49.980448+00:00",
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-PCRRep2-BinB_S38_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4004OCJK/",
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            ],
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            "creation_timestamp": "2024-11-22T06:18:51.374780+00:00",
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            },
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            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-PCRRep1-BinB_S14_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5438YNQO/",
            "accession": "IGVFFI5438YNQO",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep5_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-22T06:26:57.338834+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6623WDMM/",
            "accession": "IGVFFI6623WDMM",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep3_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2024-11-22T06:22:48.011704+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9003OVDO/",
            "accession": "IGVFFI9003OVDO",
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                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep4_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-22T06:24:57.726589+00:00",
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            },
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            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-PCRRep4-BinB_S86_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6431LCJA/",
            "accession": "IGVFFI6431LCJA",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep6_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-22T06:29:01.562355+00:00",
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            },
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            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-PCRRep6-BinB_S134_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2836PSYE/",
            "accession": "IGVFFI2836PSYE",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep8_R1"
            ],
            "content_type": "reads",
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        },
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            "@id": "/sequence-files/IGVFFI9659HSEI/",
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                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep3_R2"
            ],
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2980IPAV/",
            "accession": "IGVFFI2980IPAV",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep6_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-22T18:58:31.996400+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7719FMIO/",
            "accession": "IGVFFI7719FMIO",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep2_R2"
            ],
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0216UNBO/",
            "accession": "IGVFFI0216UNBO",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep4_R2"
            ],
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            "controlled_access": false,
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            },
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            "submitted_file_name": "Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-PCRRep4-BinB_S86_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0284EXJD/",
            "accession": "IGVFFI0284EXJD",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-BinB-PCRRep5_R2"
            ],
            "content_type": "reads",
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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/IGVFSM1469NQHM/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1469NQHM",
            "aliases": [
                "jesse-engreitz:Jurkat_Stim-IL2RA_prom-BioRep2-FFRep1-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": "2024-11-22T06:18:51.374780+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": "7b03303b-c079-462c-98b9-d576a6db39e9"
}