IGVFDS5699JBLV

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5699JBLV/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5699JBLV",
    "aliases": [
        "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_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 [IGVFSM4853BCZC](/in-vitro-systems/IGVFSM4853BCZC/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM4853BCZC/"
            },
            {
                "category": "mismatched status",
                "detail": "Released measurement set [IGVFDS5699JBLV](/measurement-sets/IGVFDS5699JBLV/) has in progress subobject auxiliary set [IGVFDS7654ZPUU](/auxiliary-sets/IGVFDS7654ZPUU/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/measurement-sets/IGVFDS5699JBLV/"
            }
        ],
        "NOT_COMPLIANT": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5699JBLV](/measurement-sets/IGVFDS5699JBLV/) 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/IGVFDS5699JBLV/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Auxiliary set [IGVFDS7654ZPUU](/auxiliary-sets/IGVFDS7654ZPUU/) has sequence file(s) [IGVFFI0928YSSZ](/sequence-files/IGVFFI0928YSSZ/), [IGVFFI3151RBXM](/sequence-files/IGVFFI3151RBXM/), [IGVFFI2700MMKU](/sequence-files/IGVFFI2700MMKU/), [IGVFFI7956SGCK](/sequence-files/IGVFFI7956SGCK/), [IGVFFI7929CUIC](/sequence-files/IGVFFI7929CUIC/), [IGVFFI9212LNJI](/sequence-files/IGVFFI9212LNJI/), [IGVFFI5994PETN](/sequence-files/IGVFFI5994PETN/), [IGVFFI5031OMIY](/sequence-files/IGVFFI5031OMIY/), [IGVFFI1803RIUO](/sequence-files/IGVFFI1803RIUO/), [IGVFFI9525HCBY](/sequence-files/IGVFFI9525HCBY/), [IGVFFI0679KMFP](/sequence-files/IGVFFI0679KMFP/), [IGVFFI6422DFEZ](/sequence-files/IGVFFI6422DFEZ/), [IGVFFI3799VBPL](/sequence-files/IGVFFI3799VBPL/), [IGVFFI7389NPMT](/sequence-files/IGVFFI7389NPMT/), [IGVFFI1992MEDA](/sequence-files/IGVFFI1992MEDA/), [IGVFFI4444PJZQ](/sequence-files/IGVFFI4444PJZQ/), [IGVFFI4146PFWX](/sequence-files/IGVFFI4146PFWX/), [IGVFFI6058ZKOZ](/sequence-files/IGVFFI6058ZKOZ/), [IGVFFI5299QRPK](/sequence-files/IGVFFI5299QRPK/), [IGVFFI6078MXLL](/sequence-files/IGVFFI6078MXLL/), [IGVFFI2920YYJS](/sequence-files/IGVFFI2920YYJS/), [IGVFFI3314MDQA](/sequence-files/IGVFFI3314MDQA/), [IGVFFI8454ZFEK](/sequence-files/IGVFFI8454ZFEK/), [IGVFFI9404WKLX](/sequence-files/IGVFFI9404WKLX/), [IGVFFI4894RVJK](/sequence-files/IGVFFI4894RVJK/), [IGVFFI6740JDUZ](/sequence-files/IGVFFI6740JDUZ/), [IGVFFI4705GOIB](/sequence-files/IGVFFI4705GOIB/), [IGVFFI9788GMPZ](/sequence-files/IGVFFI9788GMPZ/), [IGVFFI6995QNIF](/sequence-files/IGVFFI6995QNIF/), [IGVFFI4306NZHI](/sequence-files/IGVFFI4306NZHI/), [IGVFFI7059RFHS](/sequence-files/IGVFFI7059RFHS/), [IGVFFI6733QYTJ](/sequence-files/IGVFFI6733QYTJ/), [IGVFFI7217MGWG](/sequence-files/IGVFFI7217MGWG/), [IGVFFI3467VZAJ](/sequence-files/IGVFFI3467VZAJ/), [IGVFFI2369NAXZ](/sequence-files/IGVFFI2369NAXZ/), [IGVFFI2733FCGF](/sequence-files/IGVFFI2733FCGF/), [IGVFFI0080MGCB](/sequence-files/IGVFFI0080MGCB/), [IGVFFI0958OCGP](/sequence-files/IGVFFI0958OCGP/), [IGVFFI4108VBGQ](/sequence-files/IGVFFI4108VBGQ/), [IGVFFI2392XLES](/sequence-files/IGVFFI2392XLES/), [IGVFFI8726PZBB](/sequence-files/IGVFFI8726PZBB/), [IGVFFI8077WXAY](/sequence-files/IGVFFI8077WXAY/), [IGVFFI9060QDZA](/sequence-files/IGVFFI9060QDZA/), [IGVFFI0543UIGI](/sequence-files/IGVFFI0543UIGI/), [IGVFFI8622NJXI](/sequence-files/IGVFFI8622NJXI/), [IGVFFI8194VCNM](/sequence-files/IGVFFI8194VCNM/), [IGVFFI4153TTDF](/sequence-files/IGVFFI4153TTDF/), [IGVFFI8335IMVS](/sequence-files/IGVFFI8335IMVS/) 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/IGVFDS7654ZPUU/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7654ZPUU](/auxiliary-sets/IGVFDS7654ZPUU/) has sequence file(s): [IGVFFI0928YSSZ](/sequence-files/IGVFFI0928YSSZ/), [IGVFFI3151RBXM](/sequence-files/IGVFFI3151RBXM/), [IGVFFI2700MMKU](/sequence-files/IGVFFI2700MMKU/), [IGVFFI7956SGCK](/sequence-files/IGVFFI7956SGCK/), [IGVFFI7929CUIC](/sequence-files/IGVFFI7929CUIC/), [IGVFFI9212LNJI](/sequence-files/IGVFFI9212LNJI/), [IGVFFI5994PETN](/sequence-files/IGVFFI5994PETN/), [IGVFFI5031OMIY](/sequence-files/IGVFFI5031OMIY/), [IGVFFI1803RIUO](/sequence-files/IGVFFI1803RIUO/), [IGVFFI9525HCBY](/sequence-files/IGVFFI9525HCBY/), [IGVFFI0679KMFP](/sequence-files/IGVFFI0679KMFP/), [IGVFFI6422DFEZ](/sequence-files/IGVFFI6422DFEZ/), [IGVFFI3799VBPL](/sequence-files/IGVFFI3799VBPL/), [IGVFFI7389NPMT](/sequence-files/IGVFFI7389NPMT/), [IGVFFI1992MEDA](/sequence-files/IGVFFI1992MEDA/), [IGVFFI4444PJZQ](/sequence-files/IGVFFI4444PJZQ/), [IGVFFI4146PFWX](/sequence-files/IGVFFI4146PFWX/), [IGVFFI6058ZKOZ](/sequence-files/IGVFFI6058ZKOZ/), [IGVFFI5299QRPK](/sequence-files/IGVFFI5299QRPK/), [IGVFFI6078MXLL](/sequence-files/IGVFFI6078MXLL/), [IGVFFI2920YYJS](/sequence-files/IGVFFI2920YYJS/), [IGVFFI3314MDQA](/sequence-files/IGVFFI3314MDQA/), [IGVFFI8454ZFEK](/sequence-files/IGVFFI8454ZFEK/), [IGVFFI9404WKLX](/sequence-files/IGVFFI9404WKLX/), [IGVFFI4894RVJK](/sequence-files/IGVFFI4894RVJK/), [IGVFFI6740JDUZ](/sequence-files/IGVFFI6740JDUZ/), [IGVFFI4705GOIB](/sequence-files/IGVFFI4705GOIB/), [IGVFFI9788GMPZ](/sequence-files/IGVFFI9788GMPZ/), [IGVFFI6995QNIF](/sequence-files/IGVFFI6995QNIF/), [IGVFFI4306NZHI](/sequence-files/IGVFFI4306NZHI/), [IGVFFI7059RFHS](/sequence-files/IGVFFI7059RFHS/), [IGVFFI6733QYTJ](/sequence-files/IGVFFI6733QYTJ/), [IGVFFI7217MGWG](/sequence-files/IGVFFI7217MGWG/), [IGVFFI3467VZAJ](/sequence-files/IGVFFI3467VZAJ/), [IGVFFI2369NAXZ](/sequence-files/IGVFFI2369NAXZ/), [IGVFFI2733FCGF](/sequence-files/IGVFFI2733FCGF/), [IGVFFI0080MGCB](/sequence-files/IGVFFI0080MGCB/), [IGVFFI0958OCGP](/sequence-files/IGVFFI0958OCGP/), [IGVFFI4108VBGQ](/sequence-files/IGVFFI4108VBGQ/), [IGVFFI2392XLES](/sequence-files/IGVFFI2392XLES/), [IGVFFI8726PZBB](/sequence-files/IGVFFI8726PZBB/), [IGVFFI8077WXAY](/sequence-files/IGVFFI8077WXAY/), [IGVFFI9060QDZA](/sequence-files/IGVFFI9060QDZA/), [IGVFFI0543UIGI](/sequence-files/IGVFFI0543UIGI/), [IGVFFI8622NJXI](/sequence-files/IGVFFI8622NJXI/), [IGVFFI8194VCNM](/sequence-files/IGVFFI8194VCNM/), [IGVFFI4153TTDF](/sequence-files/IGVFFI4153TTDF/), [IGVFFI8335IMVS](/sequence-files/IGVFFI8335IMVS/) 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/IGVFDS7654ZPUU/"
            }
        ],
        "WARNING": [
            {
                "category": "missing analysis",
                "detail": "Auxiliary set [IGVFDS7654ZPUU](/auxiliary-sets/IGVFDS7654ZPUU/) 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/IGVFDS7654ZPUU/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS7654ZPUU/",
            "accession": "IGVFDS7654ZPUU",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC_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/IGVFDS5864UGFT/",
            "accession": "IGVFDS5864UGFT",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
            ]
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-30T22:50:11.952828+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/IGVFDS3423PSID/"
    ],
    "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": "2023-12-20T23:06:30.831593+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM4853BCZC/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4853BCZC",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep2-FFrep4-BinC"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6982DESN/",
                    "accession": "IGVFDS6982DESN",
                    "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 51-75% 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": "2023-12-05T23:11:44.061108+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": "ccdaef89-94d9-4c10-b7cb-1153308374ae"
}