IGVFDS4371VPAL

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS4371VPAL/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS4371VPAL",
    "aliases": [
        "jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM8276OEZZ](/in-vitro-systems/IGVFSM8276OEZZ/) 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/IGVFSM8276OEZZ/"
            },
            {
                "category": "mismatched status",
                "detail": "Released measurement set [IGVFDS4371VPAL](/measurement-sets/IGVFDS4371VPAL/) has in progress subobject auxiliary set [IGVFDS4456IVIM](/auxiliary-sets/IGVFDS4456IVIM/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS4371VPAL/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS4371VPAL](/measurement-sets/IGVFDS4371VPAL/) 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": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS4371VPAL/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS4456IVIM](/auxiliary-sets/IGVFDS4456IVIM/) has sequence file(s) [IGVFFI7550GRJG](/sequence-files/IGVFFI7550GRJG/), [IGVFFI7374ZSED](/sequence-files/IGVFFI7374ZSED/), [IGVFFI0117NBZL](/sequence-files/IGVFFI0117NBZL/), [IGVFFI3039FKTK](/sequence-files/IGVFFI3039FKTK/), [IGVFFI8475QQEU](/sequence-files/IGVFFI8475QQEU/), [IGVFFI7253LKOT](/sequence-files/IGVFFI7253LKOT/), [IGVFFI6275AJST](/sequence-files/IGVFFI6275AJST/), [IGVFFI3763TROO](/sequence-files/IGVFFI3763TROO/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS4456IVIM/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS4456IVIM](/auxiliary-sets/IGVFDS4456IVIM/) has sequence file(s): [IGVFFI7550GRJG](/sequence-files/IGVFFI7550GRJG/), [IGVFFI7374ZSED](/sequence-files/IGVFFI7374ZSED/), [IGVFFI0117NBZL](/sequence-files/IGVFFI0117NBZL/), [IGVFFI3039FKTK](/sequence-files/IGVFFI3039FKTK/), [IGVFFI8475QQEU](/sequence-files/IGVFFI8475QQEU/), [IGVFFI7253LKOT](/sequence-files/IGVFFI7253LKOT/), [IGVFFI6275AJST](/sequence-files/IGVFFI6275AJST/), [IGVFFI3763TROO](/sequence-files/IGVFFI3763TROO/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS4456IVIM/"
            }
        ],
        "WARNING": [
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS4456IVIM](/auxiliary-sets/IGVFDS4456IVIM/) is a raw data set with files, but is not listed in any `input_file_sets` for any analysis sets. Raw data sets with files are expected to be associated with at least one analysis set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_input_for",
                "path": "/auxiliary-sets/IGVFDS4456IVIM/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS4456IVIM/",
            "accession": "IGVFDS4456IVIM",
            "aliases": [
                "jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinD_AmpliconSequencing_AuxiliarySet"
            ],
            "file_set_type": "variant sequencing"
        }
    ],
    "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/IGVFDS6385JXFZ/",
            "accession": "IGVFDS6385JXFZ",
            "aliases": [
                "jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-THP1-PE2_Exp3_NegControl_AmpliconSequencing"
            ]
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-30T22:45:58.237794+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7359LVPI/",
            "accession": "IGVFDO7359LVPI",
            "aliases": [
                "igvf:donor_of_THP1"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [],
    "input_for": [
        "/analysis-sets/IGVFDS5056OAGR/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set.",
    "preferred_assay_title": "Variant FlowFISH",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "release_timestamp": "2023-12-20T23:09:32.092116+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8276OEZZ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8276OEZZ",
            "aliases": [
                "jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep1-FFrep2-BinD"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6377KNCH/",
                    "accession": "IGVFDS6377KNCH",
                    "file_set_type": "guide library",
                    "summary": "Guide (sgRNA) library targeting sequence variants in a genomic locus"
                }
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
                    "modality": "prime editing"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0001253/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:THP-1"
                    ],
                    "status": "released",
                    "summary": "THP-1",
                    "term_name": "THP-1"
                }
            ],
            "status": "released",
            "summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "22",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T18:25:33.494745+00:00",
    "summary": "prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000108179/",
            "geneid": "ENSG00000108179",
            "name": "peptidylprolyl isomerase F",
            "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": "4a67510b-ac98-4944-8205-307dc10eb25b"
}