IGVFDS9207WJXA

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS9207WJXA/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9207WJXA",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-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": "Released in vitro system [IGVFSM9197ZOVQ](/in-vitro-systems/IGVFSM9197ZOVQ/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM9197ZOVQ/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS9207WJXA](/measurement-sets/IGVFDS9207WJXA/) has sequence file(s) [IGVFFI1754HZPM](/sequence-files/IGVFFI1754HZPM/), [IGVFFI2917DFMT](/sequence-files/IGVFFI2917DFMT/), [IGVFFI3068SLVP](/sequence-files/IGVFFI3068SLVP/), [IGVFFI0306TJPD](/sequence-files/IGVFFI0306TJPD/), [IGVFFI1299DILF](/sequence-files/IGVFFI1299DILF/), [IGVFFI9446IVHR](/sequence-files/IGVFFI9446IVHR/), [IGVFFI7216KWXD](/sequence-files/IGVFFI7216KWXD/), [IGVFFI0080JRSY](/sequence-files/IGVFFI0080JRSY/) 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/IGVFDS9207WJXA/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS9207WJXA](/measurement-sets/IGVFDS9207WJXA/) has sequence file(s): [IGVFFI1754HZPM](/sequence-files/IGVFFI1754HZPM/), [IGVFFI2917DFMT](/sequence-files/IGVFFI2917DFMT/), [IGVFFI3068SLVP](/sequence-files/IGVFFI3068SLVP/), [IGVFFI0306TJPD](/sequence-files/IGVFFI0306TJPD/), [IGVFFI1299DILF](/sequence-files/IGVFFI1299DILF/), [IGVFFI9446IVHR](/sequence-files/IGVFFI9446IVHR/), [IGVFFI7216KWXD](/sequence-files/IGVFFI7216KWXD/), [IGVFFI0080JRSY](/sequence-files/IGVFFI0080JRSY/) 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/IGVFDS9207WJXA/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS9207WJXA](/measurement-sets/IGVFDS9207WJXA/) 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/IGVFDS9207WJXA/"
            }
        ]
    },
    "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/IGVFDS9477ARWI/",
            "accession": "IGVFDS9477ARWI",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-30T22:48:19.144579+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",
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                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:08:16.087296+00:00",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep2_S199_R1_001.fastq.gz",
            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI2917DFMT/",
            "accession": "IGVFFI2917DFMT",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:25:09.462843+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3068SLVP/",
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            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:16:41.482314+00:00",
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                "status": "released",
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            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep2_S199_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0306TJPD/",
            "accession": "IGVFFI0306TJPD",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:35:04.623737+00:00",
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            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep1_S142_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1299DILF/",
            "accession": "IGVFFI1299DILF",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:51:55.836416+00:00",
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            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep1_S142_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9446IVHR/",
            "accession": "IGVFFI9446IVHR",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:33:21.811086+00:00",
            "file_format": "fastq",
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                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep2_S199_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7216KWXD/",
            "accession": "IGVFFI7216KWXD",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:43:30.074263+00:00",
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            "sequencing_platform": {
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                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep1_S142_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0080JRSY/",
            "accession": "IGVFFI0080JRSY",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:00:02.949490+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S17-BioRep3-FFRep1-BinB-PCRrep1_S142_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1863TJOE/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. 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"
    ],
    "release_timestamp": "2023-12-20T23:04:19.213383+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9197ZOVQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9197ZOVQ",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep1-BinB"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6377KNCH/",
                    "accession": "IGVFDS6377KNCH",
                    "file_set_type": "guide library",
                    "status": "in progress",
                    "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": "released",
            "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 11-20% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/df02c0d4-f796-4f77-bfbc-388cdbfcc615/",
                    "status": "released",
                    "treatment_term_name": "T-cell surface glycoprotein CD3 gamma chain"
                },
                {
                    "@id": "/treatments/42b3c61d-38de-4bd2-bb39-33c125a417cb/",
                    "status": "released",
                    "treatment_term_name": "phorbol 13-acetate 12-myristate"
                }
            ]
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T19:35:04.623737+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": "7b11f820-6f83-4109-9045-7afbfd20e2d1"
}