IGVFDS5752WCRU

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5752WCRU/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5752WCRU",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinC_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 [IGVFDS5752WCRU](/measurement-sets/IGVFDS5752WCRU/) has sequence file(s) [IGVFFI8941FHLN](/sequence-files/IGVFFI8941FHLN/), [IGVFFI7063EOFS](/sequence-files/IGVFFI7063EOFS/), [IGVFFI6276FRYO](/sequence-files/IGVFFI6276FRYO/), [IGVFFI9576IXOX](/sequence-files/IGVFFI9576IXOX/), [IGVFFI4522QWFP](/sequence-files/IGVFFI4522QWFP/), [IGVFFI7191NJRV](/sequence-files/IGVFFI7191NJRV/), [IGVFFI5644VYAQ](/sequence-files/IGVFFI5644VYAQ/), [IGVFFI4188FQQB](/sequence-files/IGVFFI4188FQQB/), [IGVFFI2732DOXD](/sequence-files/IGVFFI2732DOXD/), [IGVFFI3892BLTR](/sequence-files/IGVFFI3892BLTR/), [IGVFFI2501VREN](/sequence-files/IGVFFI2501VREN/), [IGVFFI3999OBGE](/sequence-files/IGVFFI3999OBGE/), [IGVFFI8684YABG](/sequence-files/IGVFFI8684YABG/), [IGVFFI5580YWXA](/sequence-files/IGVFFI5580YWXA/), [IGVFFI1263DKDS](/sequence-files/IGVFFI1263DKDS/), [IGVFFI1893VFYB](/sequence-files/IGVFFI1893VFYB/), [IGVFFI3454JLFG](/sequence-files/IGVFFI3454JLFG/), [IGVFFI9815YIID](/sequence-files/IGVFFI9815YIID/), [IGVFFI3933ZUOL](/sequence-files/IGVFFI3933ZUOL/), [IGVFFI5265VEFY](/sequence-files/IGVFFI5265VEFY/), [IGVFFI4297WMUV](/sequence-files/IGVFFI4297WMUV/), [IGVFFI4885XJAR](/sequence-files/IGVFFI4885XJAR/), [IGVFFI0908OOTX](/sequence-files/IGVFFI0908OOTX/), [IGVFFI6032HNPE](/sequence-files/IGVFFI6032HNPE/), [IGVFFI5960ZCDP](/sequence-files/IGVFFI5960ZCDP/), [IGVFFI4774SGQO](/sequence-files/IGVFFI4774SGQO/), [IGVFFI0150PRYU](/sequence-files/IGVFFI0150PRYU/), [IGVFFI1236KEYQ](/sequence-files/IGVFFI1236KEYQ/), [IGVFFI0372KWJH](/sequence-files/IGVFFI0372KWJH/), [IGVFFI8053BGTW](/sequence-files/IGVFFI8053BGTW/), [IGVFFI2646CXDP](/sequence-files/IGVFFI2646CXDP/), [IGVFFI3422DMRD](/sequence-files/IGVFFI3422DMRD/), [IGVFFI1790KNJY](/sequence-files/IGVFFI1790KNJY/), [IGVFFI3233JWYV](/sequence-files/IGVFFI3233JWYV/), [IGVFFI3309NVTO](/sequence-files/IGVFFI3309NVTO/), [IGVFFI5457BEBR](/sequence-files/IGVFFI5457BEBR/), [IGVFFI8444HAPQ](/sequence-files/IGVFFI8444HAPQ/), [IGVFFI5951DCNI](/sequence-files/IGVFFI5951DCNI/), [IGVFFI8305YRWN](/sequence-files/IGVFFI8305YRWN/), [IGVFFI7787PEMK](/sequence-files/IGVFFI7787PEMK/), [IGVFFI3756LRPM](/sequence-files/IGVFFI3756LRPM/), [IGVFFI2194ETYQ](/sequence-files/IGVFFI2194ETYQ/), [IGVFFI4482FCWE](/sequence-files/IGVFFI4482FCWE/), [IGVFFI0577IBTP](/sequence-files/IGVFFI0577IBTP/), [IGVFFI5785XJEW](/sequence-files/IGVFFI5785XJEW/), [IGVFFI2593VOVB](/sequence-files/IGVFFI2593VOVB/), [IGVFFI5477AQIH](/sequence-files/IGVFFI5477AQIH/), [IGVFFI1590OQWL](/sequence-files/IGVFFI1590OQWL/) 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/IGVFDS5752WCRU/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5752WCRU](/measurement-sets/IGVFDS5752WCRU/) has sequence file(s): [IGVFFI8941FHLN](/sequence-files/IGVFFI8941FHLN/), [IGVFFI7063EOFS](/sequence-files/IGVFFI7063EOFS/), [IGVFFI6276FRYO](/sequence-files/IGVFFI6276FRYO/), [IGVFFI9576IXOX](/sequence-files/IGVFFI9576IXOX/), [IGVFFI4522QWFP](/sequence-files/IGVFFI4522QWFP/), [IGVFFI7191NJRV](/sequence-files/IGVFFI7191NJRV/), [IGVFFI5644VYAQ](/sequence-files/IGVFFI5644VYAQ/), [IGVFFI4188FQQB](/sequence-files/IGVFFI4188FQQB/), [IGVFFI2732DOXD](/sequence-files/IGVFFI2732DOXD/), [IGVFFI3892BLTR](/sequence-files/IGVFFI3892BLTR/), [IGVFFI2501VREN](/sequence-files/IGVFFI2501VREN/), [IGVFFI3999OBGE](/sequence-files/IGVFFI3999OBGE/), [IGVFFI8684YABG](/sequence-files/IGVFFI8684YABG/), [IGVFFI5580YWXA](/sequence-files/IGVFFI5580YWXA/), [IGVFFI1263DKDS](/sequence-files/IGVFFI1263DKDS/), [IGVFFI1893VFYB](/sequence-files/IGVFFI1893VFYB/), [IGVFFI3454JLFG](/sequence-files/IGVFFI3454JLFG/), [IGVFFI9815YIID](/sequence-files/IGVFFI9815YIID/), [IGVFFI3933ZUOL](/sequence-files/IGVFFI3933ZUOL/), [IGVFFI5265VEFY](/sequence-files/IGVFFI5265VEFY/), [IGVFFI4297WMUV](/sequence-files/IGVFFI4297WMUV/), [IGVFFI4885XJAR](/sequence-files/IGVFFI4885XJAR/), [IGVFFI0908OOTX](/sequence-files/IGVFFI0908OOTX/), [IGVFFI6032HNPE](/sequence-files/IGVFFI6032HNPE/), [IGVFFI5960ZCDP](/sequence-files/IGVFFI5960ZCDP/), [IGVFFI4774SGQO](/sequence-files/IGVFFI4774SGQO/), [IGVFFI0150PRYU](/sequence-files/IGVFFI0150PRYU/), [IGVFFI1236KEYQ](/sequence-files/IGVFFI1236KEYQ/), [IGVFFI0372KWJH](/sequence-files/IGVFFI0372KWJH/), [IGVFFI8053BGTW](/sequence-files/IGVFFI8053BGTW/), [IGVFFI2646CXDP](/sequence-files/IGVFFI2646CXDP/), [IGVFFI3422DMRD](/sequence-files/IGVFFI3422DMRD/), [IGVFFI1790KNJY](/sequence-files/IGVFFI1790KNJY/), [IGVFFI3233JWYV](/sequence-files/IGVFFI3233JWYV/), [IGVFFI3309NVTO](/sequence-files/IGVFFI3309NVTO/), [IGVFFI5457BEBR](/sequence-files/IGVFFI5457BEBR/), [IGVFFI8444HAPQ](/sequence-files/IGVFFI8444HAPQ/), [IGVFFI5951DCNI](/sequence-files/IGVFFI5951DCNI/), [IGVFFI8305YRWN](/sequence-files/IGVFFI8305YRWN/), [IGVFFI7787PEMK](/sequence-files/IGVFFI7787PEMK/), [IGVFFI3756LRPM](/sequence-files/IGVFFI3756LRPM/), [IGVFFI2194ETYQ](/sequence-files/IGVFFI2194ETYQ/), [IGVFFI4482FCWE](/sequence-files/IGVFFI4482FCWE/), [IGVFFI0577IBTP](/sequence-files/IGVFFI0577IBTP/), [IGVFFI5785XJEW](/sequence-files/IGVFFI5785XJEW/), [IGVFFI2593VOVB](/sequence-files/IGVFFI2593VOVB/), [IGVFFI5477AQIH](/sequence-files/IGVFFI5477AQIH/), [IGVFFI1590OQWL](/sequence-files/IGVFFI1590OQWL/) 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/IGVFDS5752WCRU/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5752WCRU](/measurement-sets/IGVFDS5752WCRU/) 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/IGVFDS5752WCRU/"
            }
        ]
    },
    "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/IGVFDS4103BJLT/",
            "accession": "IGVFDS4103BJLT",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-THP1-PE2_Exp4_NegControl_AmpliconSequencing"
            ],
            "status": "preview"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-11-25T23:53:12.877589+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",
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            "@id": "/sequence-files/IGVFFI8941FHLN/",
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            ],
            "content_type": "reads",
            "controlled_access": false,
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI7063EOFS/",
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        },
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            "@id": "/sequence-files/IGVFFI6276FRYO/",
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            },
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI3892BLTR/",
            "accession": "IGVFFI3892BLTR",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
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            },
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            "upload_status": "validated"
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep4_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T17:20:58.633547+00:00",
            "file_format": "fastq",
            "file_size": 6107453,
            "href": "/sequence-files/IGVFFI5477AQIH/@@download/IGVFFI5477AQIH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/8d36da91-63d7-4d1c-bc89-7a5b9987ba70/IGVFFI5477AQIH.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep4_S586_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1590OQWL/",
            "accession": "IGVFFI1590OQWL",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep12_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T17:40:38.061544+00:00",
            "file_format": "fastq",
            "file_size": 6793611,
            "href": "/sequence-files/IGVFFI1590OQWL/@@download/IGVFFI1590OQWL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/39fbf38c-3c27-40c2-9b44-659cbf343b75/IGVFFI1590OQWL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinC-PCRrep12_S594_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS4833ZRTZ/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "notes": "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"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM0996JAYD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0996JAYD",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinC"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS4955GEYO/",
                    "accession": "IGVFDS4955GEYO",
                    "file_set_type": "guide library",
                    "status": "preview",
                    "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_0001253/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:THP-1"
                    ],
                    "status": "released",
                    "summary": "THP-1",
                    "term_name": "THP-1"
                }
            ],
            "status": "preview",
            "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": "23",
    "status": "preview",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2024-11-26T06:55:44.955383+00:00",
    "summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000108179/",
            "geneid": "ENSG00000108179",
            "name": "peptidylprolyl isomerase F",
            "status": "released",
            "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": "eeef85bf-df17-45c7-b823-b8f358819ac1"
}