IGVFDS5341DFHM

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5341DFHM/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5341DFHM",
    "aliases": [
        "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-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 measurement set [IGVFDS5341DFHM](/measurement-sets/IGVFDS5341DFHM/) has in progress subobject auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS5341DFHM/"
            },
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM3794OZOG](/in-vitro-systems/IGVFSM3794OZOG/) has in progress subobject construct library set [IGVFDS2374NXLW](/construct-library-sets/IGVFDS2374NXLW/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM3794OZOG/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5341DFHM](/measurement-sets/IGVFDS5341DFHM/) 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/IGVFDS5341DFHM/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/) has sequence file(s): [IGVFFI5675NIUY](/sequence-files/IGVFFI5675NIUY/), [IGVFFI1090NFMB](/sequence-files/IGVFFI1090NFMB/), [IGVFFI3703EBTL](/sequence-files/IGVFFI3703EBTL/), [IGVFFI4309DAPG](/sequence-files/IGVFFI4309DAPG/), [IGVFFI5608LBWW](/sequence-files/IGVFFI5608LBWW/), [IGVFFI3527ETOI](/sequence-files/IGVFFI3527ETOI/), [IGVFFI3217BFXA](/sequence-files/IGVFFI3217BFXA/), [IGVFFI6414PJUV](/sequence-files/IGVFFI6414PJUV/), [IGVFFI1341MLBR](/sequence-files/IGVFFI1341MLBR/), [IGVFFI6409ZHPQ](/sequence-files/IGVFFI6409ZHPQ/), [IGVFFI6084BLGQ](/sequence-files/IGVFFI6084BLGQ/), [IGVFFI4314REOB](/sequence-files/IGVFFI4314REOB/), [IGVFFI1205AZHU](/sequence-files/IGVFFI1205AZHU/), [IGVFFI0489BVLU](/sequence-files/IGVFFI0489BVLU/), [IGVFFI2951KQUX](/sequence-files/IGVFFI2951KQUX/), [IGVFFI1582JZJA](/sequence-files/IGVFFI1582JZJA/), [IGVFFI1656UOEF](/sequence-files/IGVFFI1656UOEF/), [IGVFFI5386FFSM](/sequence-files/IGVFFI5386FFSM/), [IGVFFI2654TOIY](/sequence-files/IGVFFI2654TOIY/), [IGVFFI5622HXWF](/sequence-files/IGVFFI5622HXWF/), [IGVFFI6020TZCV](/sequence-files/IGVFFI6020TZCV/), [IGVFFI8497HABY](/sequence-files/IGVFFI8497HABY/), [IGVFFI4619NIRP](/sequence-files/IGVFFI4619NIRP/), [IGVFFI0908HNBD](/sequence-files/IGVFFI0908HNBD/), [IGVFFI7892JUHM](/sequence-files/IGVFFI7892JUHM/), [IGVFFI5751TCVS](/sequence-files/IGVFFI5751TCVS/), [IGVFFI4689NQNE](/sequence-files/IGVFFI4689NQNE/), [IGVFFI3678MOEY](/sequence-files/IGVFFI3678MOEY/), [IGVFFI0332BJPV](/sequence-files/IGVFFI0332BJPV/), [IGVFFI8367FUZD](/sequence-files/IGVFFI8367FUZD/), [IGVFFI2995ZRFH](/sequence-files/IGVFFI2995ZRFH/), [IGVFFI0226HZOX](/sequence-files/IGVFFI0226HZOX/), [IGVFFI8967BWYO](/sequence-files/IGVFFI8967BWYO/), [IGVFFI5821YZCD](/sequence-files/IGVFFI5821YZCD/), [IGVFFI9504WNOR](/sequence-files/IGVFFI9504WNOR/), [IGVFFI1673HCRO](/sequence-files/IGVFFI1673HCRO/), [IGVFFI7364VDTT](/sequence-files/IGVFFI7364VDTT/), [IGVFFI6948SGDC](/sequence-files/IGVFFI6948SGDC/), [IGVFFI4903LWUG](/sequence-files/IGVFFI4903LWUG/), [IGVFFI3610MGBE](/sequence-files/IGVFFI3610MGBE/), [IGVFFI2355CGWD](/sequence-files/IGVFFI2355CGWD/), [IGVFFI9856HIMF](/sequence-files/IGVFFI9856HIMF/), [IGVFFI8325DPGJ](/sequence-files/IGVFFI8325DPGJ/), [IGVFFI2275NISI](/sequence-files/IGVFFI2275NISI/), [IGVFFI4980UAMK](/sequence-files/IGVFFI4980UAMK/), [IGVFFI0547HKKZ](/sequence-files/IGVFFI0547HKKZ/), [IGVFFI1555KDXH](/sequence-files/IGVFFI1555KDXH/), [IGVFFI1154KTEF](/sequence-files/IGVFFI1154KTEF/) 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/IGVFDS9278ESDK/"
            }
        ],
        "WARNING": [
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/) has sequence file(s) [IGVFFI5675NIUY](/sequence-files/IGVFFI5675NIUY/), [IGVFFI1090NFMB](/sequence-files/IGVFFI1090NFMB/), [IGVFFI3703EBTL](/sequence-files/IGVFFI3703EBTL/), [IGVFFI4309DAPG](/sequence-files/IGVFFI4309DAPG/), [IGVFFI5608LBWW](/sequence-files/IGVFFI5608LBWW/), [IGVFFI3527ETOI](/sequence-files/IGVFFI3527ETOI/), [IGVFFI3217BFXA](/sequence-files/IGVFFI3217BFXA/), [IGVFFI6414PJUV](/sequence-files/IGVFFI6414PJUV/), [IGVFFI1341MLBR](/sequence-files/IGVFFI1341MLBR/), [IGVFFI6409ZHPQ](/sequence-files/IGVFFI6409ZHPQ/), [IGVFFI6084BLGQ](/sequence-files/IGVFFI6084BLGQ/), [IGVFFI4314REOB](/sequence-files/IGVFFI4314REOB/), [IGVFFI1205AZHU](/sequence-files/IGVFFI1205AZHU/), [IGVFFI0489BVLU](/sequence-files/IGVFFI0489BVLU/), [IGVFFI2951KQUX](/sequence-files/IGVFFI2951KQUX/), [IGVFFI1582JZJA](/sequence-files/IGVFFI1582JZJA/), [IGVFFI1656UOEF](/sequence-files/IGVFFI1656UOEF/), [IGVFFI5386FFSM](/sequence-files/IGVFFI5386FFSM/), [IGVFFI2654TOIY](/sequence-files/IGVFFI2654TOIY/), [IGVFFI5622HXWF](/sequence-files/IGVFFI5622HXWF/), [IGVFFI6020TZCV](/sequence-files/IGVFFI6020TZCV/), [IGVFFI8497HABY](/sequence-files/IGVFFI8497HABY/), [IGVFFI4619NIRP](/sequence-files/IGVFFI4619NIRP/), [IGVFFI0908HNBD](/sequence-files/IGVFFI0908HNBD/), [IGVFFI7892JUHM](/sequence-files/IGVFFI7892JUHM/), [IGVFFI5751TCVS](/sequence-files/IGVFFI5751TCVS/), [IGVFFI4689NQNE](/sequence-files/IGVFFI4689NQNE/), [IGVFFI3678MOEY](/sequence-files/IGVFFI3678MOEY/), [IGVFFI0332BJPV](/sequence-files/IGVFFI0332BJPV/), [IGVFFI8367FUZD](/sequence-files/IGVFFI8367FUZD/), [IGVFFI2995ZRFH](/sequence-files/IGVFFI2995ZRFH/), [IGVFFI0226HZOX](/sequence-files/IGVFFI0226HZOX/), [IGVFFI8967BWYO](/sequence-files/IGVFFI8967BWYO/), [IGVFFI5821YZCD](/sequence-files/IGVFFI5821YZCD/), [IGVFFI9504WNOR](/sequence-files/IGVFFI9504WNOR/), [IGVFFI1673HCRO](/sequence-files/IGVFFI1673HCRO/), [IGVFFI7364VDTT](/sequence-files/IGVFFI7364VDTT/), [IGVFFI6948SGDC](/sequence-files/IGVFFI6948SGDC/), [IGVFFI4903LWUG](/sequence-files/IGVFFI4903LWUG/), [IGVFFI3610MGBE](/sequence-files/IGVFFI3610MGBE/), [IGVFFI2355CGWD](/sequence-files/IGVFFI2355CGWD/), [IGVFFI9856HIMF](/sequence-files/IGVFFI9856HIMF/), [IGVFFI8325DPGJ](/sequence-files/IGVFFI8325DPGJ/), [IGVFFI2275NISI](/sequence-files/IGVFFI2275NISI/), [IGVFFI4980UAMK](/sequence-files/IGVFFI4980UAMK/), [IGVFFI0547HKKZ](/sequence-files/IGVFFI0547HKKZ/), [IGVFFI1555KDXH](/sequence-files/IGVFFI1555KDXH/), [IGVFFI1154KTEF](/sequence-files/IGVFFI1154KTEF/) 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/IGVFDS9278ESDK/"
            },
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS9278ESDK](/auxiliary-sets/IGVFDS9278ESDK/) 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/IGVFDS9278ESDK/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS9278ESDK/",
            "accession": "IGVFDS9278ESDK",
            "aliases": [
                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-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/IGVFDS4989HPTW/",
            "accession": "IGVFDS4989HPTW",
            "aliases": [
                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-THP1-PE2_Exp1_NegControl_AmpliconSequencing"
            ]
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-30T22:48:59.649835+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/IGVFDS5031MNRR/"
    ],
    "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": "2023-12-20T23:05:18.727434+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3794OZOG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3794OZOG",
            "aliases": [
                "jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep1-FFrep3-BinB"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2374NXLW/",
                    "accession": "IGVFDS2374NXLW",
                    "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": "21",
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T20:23:06.062286+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": "948acf22-b623-479d-bd7a-f1286250dcc4"
}