IGVFDS9880SAMJ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS9880SAMJ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS9880SAMJ",
    "aliases": [
        "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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 [IGVFSM0425HXKG](/in-vitro-systems/IGVFSM0425HXKG/) has in progress subobject construct library set [IGVFDS2385DHZO](/construct-library-sets/IGVFDS2385DHZO/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM0425HXKG/"
            },
            {
                "category": "mismatched status",
                "detail": "Released measurement set [IGVFDS9880SAMJ](/measurement-sets/IGVFDS9880SAMJ/) has in progress subobject auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS9880SAMJ/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS9880SAMJ](/measurement-sets/IGVFDS9880SAMJ/) 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/IGVFDS9880SAMJ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/) has sequence file(s): [IGVFFI5237WXKT](/sequence-files/IGVFFI5237WXKT/), [IGVFFI8045DBRH](/sequence-files/IGVFFI8045DBRH/), [IGVFFI5303UWCW](/sequence-files/IGVFFI5303UWCW/), [IGVFFI4938XQQC](/sequence-files/IGVFFI4938XQQC/), [IGVFFI8971RNCP](/sequence-files/IGVFFI8971RNCP/), [IGVFFI0639DLTP](/sequence-files/IGVFFI0639DLTP/), [IGVFFI7814STZZ](/sequence-files/IGVFFI7814STZZ/), [IGVFFI5766UGKA](/sequence-files/IGVFFI5766UGKA/), [IGVFFI5341CZHN](/sequence-files/IGVFFI5341CZHN/), [IGVFFI3891XOWU](/sequence-files/IGVFFI3891XOWU/), [IGVFFI5216WORF](/sequence-files/IGVFFI5216WORF/), [IGVFFI9538UKYI](/sequence-files/IGVFFI9538UKYI/), [IGVFFI7370FGAL](/sequence-files/IGVFFI7370FGAL/), [IGVFFI6678KRCD](/sequence-files/IGVFFI6678KRCD/), [IGVFFI6185PUPQ](/sequence-files/IGVFFI6185PUPQ/), [IGVFFI8802CEYE](/sequence-files/IGVFFI8802CEYE/), [IGVFFI1837CZNX](/sequence-files/IGVFFI1837CZNX/), [IGVFFI1549SYKV](/sequence-files/IGVFFI1549SYKV/), [IGVFFI3668BISN](/sequence-files/IGVFFI3668BISN/), [IGVFFI0500TLSN](/sequence-files/IGVFFI0500TLSN/), [IGVFFI1987FBOD](/sequence-files/IGVFFI1987FBOD/), [IGVFFI3414UQDV](/sequence-files/IGVFFI3414UQDV/), [IGVFFI2255CQUA](/sequence-files/IGVFFI2255CQUA/), [IGVFFI8058JFNA](/sequence-files/IGVFFI8058JFNA/), [IGVFFI9114FXPF](/sequence-files/IGVFFI9114FXPF/), [IGVFFI7451BWUU](/sequence-files/IGVFFI7451BWUU/), [IGVFFI4142CJON](/sequence-files/IGVFFI4142CJON/), [IGVFFI1575FIKC](/sequence-files/IGVFFI1575FIKC/), [IGVFFI4077YUEX](/sequence-files/IGVFFI4077YUEX/), [IGVFFI9222FTVM](/sequence-files/IGVFFI9222FTVM/), [IGVFFI3993LSKG](/sequence-files/IGVFFI3993LSKG/), [IGVFFI2766XRSC](/sequence-files/IGVFFI2766XRSC/), [IGVFFI8924DLZG](/sequence-files/IGVFFI8924DLZG/), [IGVFFI8350ONYK](/sequence-files/IGVFFI8350ONYK/), [IGVFFI3089ONQN](/sequence-files/IGVFFI3089ONQN/), [IGVFFI3185IEQB](/sequence-files/IGVFFI3185IEQB/), [IGVFFI2196KYUA](/sequence-files/IGVFFI2196KYUA/), [IGVFFI1926BWQM](/sequence-files/IGVFFI1926BWQM/), [IGVFFI4321AQUF](/sequence-files/IGVFFI4321AQUF/), [IGVFFI8445SUJK](/sequence-files/IGVFFI8445SUJK/), [IGVFFI6907KVFS](/sequence-files/IGVFFI6907KVFS/), [IGVFFI0641VMHM](/sequence-files/IGVFFI0641VMHM/), [IGVFFI8394NWWI](/sequence-files/IGVFFI8394NWWI/), [IGVFFI3553BQUL](/sequence-files/IGVFFI3553BQUL/), [IGVFFI3360YTGE](/sequence-files/IGVFFI3360YTGE/), [IGVFFI5501FITI](/sequence-files/IGVFFI5501FITI/), [IGVFFI1042LQUB](/sequence-files/IGVFFI1042LQUB/), [IGVFFI6432BOCW](/sequence-files/IGVFFI6432BOCW/) 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/IGVFDS3877HUJV/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/) has sequence file(s) [IGVFFI5237WXKT](/sequence-files/IGVFFI5237WXKT/), [IGVFFI8045DBRH](/sequence-files/IGVFFI8045DBRH/), [IGVFFI5303UWCW](/sequence-files/IGVFFI5303UWCW/), [IGVFFI4938XQQC](/sequence-files/IGVFFI4938XQQC/), [IGVFFI8971RNCP](/sequence-files/IGVFFI8971RNCP/), [IGVFFI0639DLTP](/sequence-files/IGVFFI0639DLTP/), [IGVFFI7814STZZ](/sequence-files/IGVFFI7814STZZ/), [IGVFFI5766UGKA](/sequence-files/IGVFFI5766UGKA/), [IGVFFI5341CZHN](/sequence-files/IGVFFI5341CZHN/), [IGVFFI3891XOWU](/sequence-files/IGVFFI3891XOWU/), [IGVFFI5216WORF](/sequence-files/IGVFFI5216WORF/), [IGVFFI9538UKYI](/sequence-files/IGVFFI9538UKYI/), [IGVFFI7370FGAL](/sequence-files/IGVFFI7370FGAL/), [IGVFFI6678KRCD](/sequence-files/IGVFFI6678KRCD/), [IGVFFI6185PUPQ](/sequence-files/IGVFFI6185PUPQ/), [IGVFFI8802CEYE](/sequence-files/IGVFFI8802CEYE/), [IGVFFI1837CZNX](/sequence-files/IGVFFI1837CZNX/), [IGVFFI1549SYKV](/sequence-files/IGVFFI1549SYKV/), [IGVFFI3668BISN](/sequence-files/IGVFFI3668BISN/), [IGVFFI0500TLSN](/sequence-files/IGVFFI0500TLSN/), [IGVFFI1987FBOD](/sequence-files/IGVFFI1987FBOD/), [IGVFFI3414UQDV](/sequence-files/IGVFFI3414UQDV/), [IGVFFI2255CQUA](/sequence-files/IGVFFI2255CQUA/), [IGVFFI8058JFNA](/sequence-files/IGVFFI8058JFNA/), [IGVFFI9114FXPF](/sequence-files/IGVFFI9114FXPF/), [IGVFFI7451BWUU](/sequence-files/IGVFFI7451BWUU/), [IGVFFI4142CJON](/sequence-files/IGVFFI4142CJON/), [IGVFFI1575FIKC](/sequence-files/IGVFFI1575FIKC/), [IGVFFI4077YUEX](/sequence-files/IGVFFI4077YUEX/), [IGVFFI9222FTVM](/sequence-files/IGVFFI9222FTVM/), [IGVFFI3993LSKG](/sequence-files/IGVFFI3993LSKG/), [IGVFFI2766XRSC](/sequence-files/IGVFFI2766XRSC/), [IGVFFI8924DLZG](/sequence-files/IGVFFI8924DLZG/), [IGVFFI8350ONYK](/sequence-files/IGVFFI8350ONYK/), [IGVFFI3089ONQN](/sequence-files/IGVFFI3089ONQN/), [IGVFFI3185IEQB](/sequence-files/IGVFFI3185IEQB/), [IGVFFI2196KYUA](/sequence-files/IGVFFI2196KYUA/), [IGVFFI1926BWQM](/sequence-files/IGVFFI1926BWQM/), [IGVFFI4321AQUF](/sequence-files/IGVFFI4321AQUF/), [IGVFFI8445SUJK](/sequence-files/IGVFFI8445SUJK/), [IGVFFI6907KVFS](/sequence-files/IGVFFI6907KVFS/), [IGVFFI0641VMHM](/sequence-files/IGVFFI0641VMHM/), [IGVFFI8394NWWI](/sequence-files/IGVFFI8394NWWI/), [IGVFFI3553BQUL](/sequence-files/IGVFFI3553BQUL/), [IGVFFI3360YTGE](/sequence-files/IGVFFI3360YTGE/), [IGVFFI5501FITI](/sequence-files/IGVFFI5501FITI/), [IGVFFI1042LQUB](/sequence-files/IGVFFI1042LQUB/), [IGVFFI6432BOCW](/sequence-files/IGVFFI6432BOCW/) which lack specification of a `sequencing_kit`. Sequence files should specify a sequencing kit.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_inconsistent_sequencing_kit",
                "path": "/auxiliary-sets/IGVFDS3877HUJV/"
            },
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS3877HUJV](/auxiliary-sets/IGVFDS3877HUJV/) 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_file_set_for",
                "path": "/auxiliary-sets/IGVFDS3877HUJV/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS3877HUJV/",
            "accession": "IGVFDS3877HUJV",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB_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/IGVFDS5128CXIS/",
            "accession": "IGVFDS5128CXIS",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
            ]
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-12-13T08:01:45.179071+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO7359LVPI/",
            "accession": "IGVFDO7359LVPI",
            "aliases": [
                "igvf:donor_of_THP1"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "experimental data",
    "files": [],
    "input_file_set_for": [
        "/analysis-sets/IGVFDS4359OODY/"
    ],
    "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": "2023-12-20T23:08:06.997920+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0425HXKG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0425HXKG",
            "aliases": [
                "jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinB"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2385DHZO/",
                    "accession": "IGVFDS2385DHZO",
                    "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 26-50% expression of PPIF) modified with a guide library",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "20",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-13T08:58:50.439180+00:00",
    "summary": "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": "fa80915b-6ed1-4719-95bc-30b16118a77f"
}