IGVFDS6090MUID

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS6090MUID/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS6090MUID",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA_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 [IGVFDS6090MUID](/measurement-sets/IGVFDS6090MUID/) has sequence file(s) [IGVFFI5656FYDJ](/sequence-files/IGVFFI5656FYDJ/), [IGVFFI8871GOPW](/sequence-files/IGVFFI8871GOPW/), [IGVFFI4743PYQP](/sequence-files/IGVFFI4743PYQP/), [IGVFFI9412CKAI](/sequence-files/IGVFFI9412CKAI/), [IGVFFI2814MFMG](/sequence-files/IGVFFI2814MFMG/), [IGVFFI9052ZZHZ](/sequence-files/IGVFFI9052ZZHZ/), [IGVFFI1431VABH](/sequence-files/IGVFFI1431VABH/), [IGVFFI6131DACM](/sequence-files/IGVFFI6131DACM/), [IGVFFI2078LSNT](/sequence-files/IGVFFI2078LSNT/), [IGVFFI9111MXIH](/sequence-files/IGVFFI9111MXIH/), [IGVFFI3769JODO](/sequence-files/IGVFFI3769JODO/), [IGVFFI9013QYSC](/sequence-files/IGVFFI9013QYSC/), [IGVFFI0707MBTB](/sequence-files/IGVFFI0707MBTB/), [IGVFFI5976IEOZ](/sequence-files/IGVFFI5976IEOZ/), [IGVFFI6752MCCF](/sequence-files/IGVFFI6752MCCF/), [IGVFFI0476BSMO](/sequence-files/IGVFFI0476BSMO/), [IGVFFI5426ELUN](/sequence-files/IGVFFI5426ELUN/), [IGVFFI0769WWGZ](/sequence-files/IGVFFI0769WWGZ/), [IGVFFI3707TENL](/sequence-files/IGVFFI3707TENL/), [IGVFFI3888LQBR](/sequence-files/IGVFFI3888LQBR/), [IGVFFI9734XPAY](/sequence-files/IGVFFI9734XPAY/), [IGVFFI3064NWJJ](/sequence-files/IGVFFI3064NWJJ/), [IGVFFI4551JRAY](/sequence-files/IGVFFI4551JRAY/), [IGVFFI8737YJQR](/sequence-files/IGVFFI8737YJQR/), [IGVFFI9289VZKY](/sequence-files/IGVFFI9289VZKY/), [IGVFFI2602RLFA](/sequence-files/IGVFFI2602RLFA/), [IGVFFI6983HHJM](/sequence-files/IGVFFI6983HHJM/), [IGVFFI2971BGOG](/sequence-files/IGVFFI2971BGOG/), [IGVFFI3242EEOO](/sequence-files/IGVFFI3242EEOO/), [IGVFFI1183GZIE](/sequence-files/IGVFFI1183GZIE/), [IGVFFI5628DMDR](/sequence-files/IGVFFI5628DMDR/), [IGVFFI0314IGQW](/sequence-files/IGVFFI0314IGQW/), [IGVFFI7104LJQM](/sequence-files/IGVFFI7104LJQM/), [IGVFFI7581BJQH](/sequence-files/IGVFFI7581BJQH/), [IGVFFI4763WLUQ](/sequence-files/IGVFFI4763WLUQ/), [IGVFFI2410UIWI](/sequence-files/IGVFFI2410UIWI/), [IGVFFI6903ABEX](/sequence-files/IGVFFI6903ABEX/), [IGVFFI8153SOGZ](/sequence-files/IGVFFI8153SOGZ/), [IGVFFI4088NJSN](/sequence-files/IGVFFI4088NJSN/), [IGVFFI3291PISX](/sequence-files/IGVFFI3291PISX/), [IGVFFI5456KGNX](/sequence-files/IGVFFI5456KGNX/), [IGVFFI9616BIIC](/sequence-files/IGVFFI9616BIIC/), [IGVFFI1805FUTP](/sequence-files/IGVFFI1805FUTP/), [IGVFFI0046KYLI](/sequence-files/IGVFFI0046KYLI/), [IGVFFI0516IUHT](/sequence-files/IGVFFI0516IUHT/), [IGVFFI7812KADG](/sequence-files/IGVFFI7812KADG/), [IGVFFI9187JPER](/sequence-files/IGVFFI9187JPER/), [IGVFFI5447INVW](/sequence-files/IGVFFI5447INVW/) 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/IGVFDS6090MUID/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS6090MUID](/measurement-sets/IGVFDS6090MUID/) has sequence file(s): [IGVFFI5656FYDJ](/sequence-files/IGVFFI5656FYDJ/), [IGVFFI8871GOPW](/sequence-files/IGVFFI8871GOPW/), [IGVFFI4743PYQP](/sequence-files/IGVFFI4743PYQP/), [IGVFFI9412CKAI](/sequence-files/IGVFFI9412CKAI/), [IGVFFI2814MFMG](/sequence-files/IGVFFI2814MFMG/), [IGVFFI9052ZZHZ](/sequence-files/IGVFFI9052ZZHZ/), [IGVFFI1431VABH](/sequence-files/IGVFFI1431VABH/), [IGVFFI6131DACM](/sequence-files/IGVFFI6131DACM/), [IGVFFI2078LSNT](/sequence-files/IGVFFI2078LSNT/), [IGVFFI9111MXIH](/sequence-files/IGVFFI9111MXIH/), [IGVFFI3769JODO](/sequence-files/IGVFFI3769JODO/), [IGVFFI9013QYSC](/sequence-files/IGVFFI9013QYSC/), [IGVFFI0707MBTB](/sequence-files/IGVFFI0707MBTB/), [IGVFFI5976IEOZ](/sequence-files/IGVFFI5976IEOZ/), [IGVFFI6752MCCF](/sequence-files/IGVFFI6752MCCF/), [IGVFFI0476BSMO](/sequence-files/IGVFFI0476BSMO/), [IGVFFI5426ELUN](/sequence-files/IGVFFI5426ELUN/), [IGVFFI0769WWGZ](/sequence-files/IGVFFI0769WWGZ/), [IGVFFI3707TENL](/sequence-files/IGVFFI3707TENL/), [IGVFFI3888LQBR](/sequence-files/IGVFFI3888LQBR/), [IGVFFI9734XPAY](/sequence-files/IGVFFI9734XPAY/), [IGVFFI3064NWJJ](/sequence-files/IGVFFI3064NWJJ/), [IGVFFI4551JRAY](/sequence-files/IGVFFI4551JRAY/), [IGVFFI8737YJQR](/sequence-files/IGVFFI8737YJQR/), [IGVFFI9289VZKY](/sequence-files/IGVFFI9289VZKY/), [IGVFFI2602RLFA](/sequence-files/IGVFFI2602RLFA/), [IGVFFI6983HHJM](/sequence-files/IGVFFI6983HHJM/), [IGVFFI2971BGOG](/sequence-files/IGVFFI2971BGOG/), [IGVFFI3242EEOO](/sequence-files/IGVFFI3242EEOO/), [IGVFFI1183GZIE](/sequence-files/IGVFFI1183GZIE/), [IGVFFI5628DMDR](/sequence-files/IGVFFI5628DMDR/), [IGVFFI0314IGQW](/sequence-files/IGVFFI0314IGQW/), [IGVFFI7104LJQM](/sequence-files/IGVFFI7104LJQM/), [IGVFFI7581BJQH](/sequence-files/IGVFFI7581BJQH/), [IGVFFI4763WLUQ](/sequence-files/IGVFFI4763WLUQ/), [IGVFFI2410UIWI](/sequence-files/IGVFFI2410UIWI/), [IGVFFI6903ABEX](/sequence-files/IGVFFI6903ABEX/), [IGVFFI8153SOGZ](/sequence-files/IGVFFI8153SOGZ/), [IGVFFI4088NJSN](/sequence-files/IGVFFI4088NJSN/), [IGVFFI3291PISX](/sequence-files/IGVFFI3291PISX/), [IGVFFI5456KGNX](/sequence-files/IGVFFI5456KGNX/), [IGVFFI9616BIIC](/sequence-files/IGVFFI9616BIIC/), [IGVFFI1805FUTP](/sequence-files/IGVFFI1805FUTP/), [IGVFFI0046KYLI](/sequence-files/IGVFFI0046KYLI/), [IGVFFI0516IUHT](/sequence-files/IGVFFI0516IUHT/), [IGVFFI7812KADG](/sequence-files/IGVFFI7812KADG/), [IGVFFI9187JPER](/sequence-files/IGVFFI9187JPER/), [IGVFFI5447INVW](/sequence-files/IGVFFI5447INVW/) 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/IGVFDS6090MUID/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS6090MUID](/measurement-sets/IGVFDS6090MUID/) 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/IGVFDS6090MUID/"
            }
        ]
    },
    "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": "2024-11-25T23:53:03.523106+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": [
        {
            "@id": "/sequence-files/IGVFFI5656FYDJ/",
            "accession": "IGVFFI5656FYDJ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep8_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:04:20.811433+00:00",
            "file_format": "fastq",
            "file_size": 14544618,
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            "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-BinA-PCRrep8_S566_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8871GOPW/",
            "accession": "IGVFFI8871GOPW",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep3_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T06:58:04.390117+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep3_S561_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4743PYQP/",
            "accession": "IGVFFI4743PYQP",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T06:55:11.149976+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep1_S559_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9412CKAI/",
            "accession": "IGVFFI9412CKAI",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep4_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2024-11-26T06:59:13.425743+00:00",
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2814MFMG/",
            "accession": "IGVFFI2814MFMG",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep6_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:01:43.385458+00:00",
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                "term_name": "Illumina NovaSeq X"
            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9052ZZHZ/",
            "accession": "IGVFFI9052ZZHZ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep7_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2024-11-26T07:03:00.520070+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1431VABH/",
            "accession": "IGVFFI1431VABH",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep5_R1"
            ],
            "content_type": "reads",
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            "creation_timestamp": "2024-11-26T07:00:24.936746+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6131DACM/",
            "accession": "IGVFFI6131DACM",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep9_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:05:44.647599+00:00",
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            },
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2078LSNT/",
            "accession": "IGVFFI2078LSNT",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep10_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:07:09.328308+00:00",
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
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            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep10_S568_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9111MXIH/",
            "accession": "IGVFFI9111MXIH",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep11_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:08:34.048683+00:00",
            "file_format": "fastq",
            "file_size": 14147654,
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            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240426S024-Enhancer-THP1-PPIF_Enhancer_val_guides-Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep11_S569_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3769JODO/",
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            "controlled_access": false,
            "creation_timestamp": "2024-11-26T17:39:20.876149+00:00",
            "file_format": "fastq",
            "file_size": 6489846,
            "href": "/sequence-files/IGVFFI9187JPER/@@download/IGVFFI9187JPER.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/32679f8a-1153-4cca-8da7-c62ebb1cbcb5/IGVFFI9187JPER.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-BinA-PCRrep12_S570_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5447INVW/",
            "accession": "IGVFFI5447INVW",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA-PCRrep8_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T17:29:37.816623+00:00",
            "file_format": "fastq",
            "file_size": 6973949,
            "href": "/sequence-files/IGVFFI5447INVW/@@download/IGVFFI5447INVW.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/6c1b2931-c3e0-42c1-a3b7-97449c755700/IGVFFI5447INVW.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-BinA-PCRrep8_S566_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/IGVFSM9224JLWC/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9224JLWC",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep4-BinA"
            ],
            "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 0-25% 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": "2024-11-26T06:55:11.149976+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": "b5392576-31b4-478b-9cad-317b2dd31c13"
}