IGVFDS0997EDUX

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0997EDUX/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0997EDUX",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input_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 [IGVFDS0997EDUX](/measurement-sets/IGVFDS0997EDUX/) has sequence file(s) [IGVFFI4006PXVH](/sequence-files/IGVFFI4006PXVH/), [IGVFFI8339KNRC](/sequence-files/IGVFFI8339KNRC/), [IGVFFI4210CUQC](/sequence-files/IGVFFI4210CUQC/), [IGVFFI3016LZCD](/sequence-files/IGVFFI3016LZCD/), [IGVFFI9430TIHE](/sequence-files/IGVFFI9430TIHE/), [IGVFFI2746BQUH](/sequence-files/IGVFFI2746BQUH/), [IGVFFI6537OQWY](/sequence-files/IGVFFI6537OQWY/), [IGVFFI5510WUVC](/sequence-files/IGVFFI5510WUVC/) 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/IGVFDS0997EDUX/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS0997EDUX](/measurement-sets/IGVFDS0997EDUX/) has sequence file(s): [IGVFFI4006PXVH](/sequence-files/IGVFFI4006PXVH/), [IGVFFI8339KNRC](/sequence-files/IGVFFI8339KNRC/), [IGVFFI4210CUQC](/sequence-files/IGVFFI4210CUQC/), [IGVFFI3016LZCD](/sequence-files/IGVFFI3016LZCD/), [IGVFFI9430TIHE](/sequence-files/IGVFFI9430TIHE/), [IGVFFI2746BQUH](/sequence-files/IGVFFI2746BQUH/), [IGVFFI6537OQWY](/sequence-files/IGVFFI6537OQWY/), [IGVFFI5510WUVC](/sequence-files/IGVFFI5510WUVC/) 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/IGVFDS0997EDUX/"
            },
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM0193KFOU](/in-vitro-systems/IGVFSM0193KFOU/) 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/IGVFSM0193KFOU/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS0997EDUX](/measurement-sets/IGVFDS0997EDUX/) 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/IGVFDS0997EDUX/"
            },
            {
                "category": "missing targeted genes",
                "detail": "Measurement set [IGVFDS0997EDUX](/measurement-sets/IGVFDS0997EDUX/) has no `targeted_genes`. ChIP-seq and CRISPR flow cytometry assays are expected to specify targeted gene(s).",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_targeted_genes",
                "path": "/measurement-sets/IGVFDS0997EDUX/"
            }
        ]
    },
    "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": [],
    "control_type": "unsorted FACS input",
    "creation_timestamp": "2023-11-30T22:48:33.685052+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-BioRep4-FFrep1-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
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            "sequencing_platform": {
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            },
            "status": "released",
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            "upload_status": "validated"
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            "@id": "/sequence-files/IGVFFI8339KNRC/",
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                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_I1"
            ],
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            "status": "released",
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            "upload_status": "validated"
        },
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            ],
            "content_type": "reads",
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            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinAll-PCRrep2_S218_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3016LZCD/",
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                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2023-12-05T20:11:04.552922+00:00",
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            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinAll-PCRrep2_S218_R1_001.fastq.gz",
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            "@id": "/sequence-files/IGVFFI9430TIHE/",
            "accession": "IGVFFI9430TIHE",
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                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_R2"
            ],
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            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinAll-PCRrep1_S161_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2746BQUH/",
            "accession": "IGVFFI2746BQUH",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:36:07.399299+00:00",
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            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinAll-PCRrep2_S218_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6537OQWY/",
            "accession": "IGVFFI6537OQWY",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:27:54.921601+00:00",
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            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinAll-PCRrep2_S218_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5510WUVC/",
            "accession": "IGVFFI5510WUVC",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input-PCRrep1_I2"
            ],
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            "controlled_access": false,
            "creation_timestamp": "2023-12-05T20:02:48.099714+00:00",
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            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S19-BioRep4-FFRep1-BinAll-PCRrep1_S161_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": "2023-12-20T23:04:48.633380+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0193KFOU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0193KFOU",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep4-FFrep1-FACS_Input"
            ],
            "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 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": "2023-12-05T19:37:52.870829+00:00",
    "summary": "unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
    "uuid": "8c26abb9-53f8-4515-86a4-e884608726ec"
}