IGVFDS7312BCBZ

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7312BCBZ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7312BCBZ",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-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 [IGVFDS7312BCBZ](/measurement-sets/IGVFDS7312BCBZ/) has sequence file(s) [IGVFFI7241XKKE](/sequence-files/IGVFFI7241XKKE/), [IGVFFI2087UMAQ](/sequence-files/IGVFFI2087UMAQ/), [IGVFFI9557VBNH](/sequence-files/IGVFFI9557VBNH/), [IGVFFI1419ZYLP](/sequence-files/IGVFFI1419ZYLP/), [IGVFFI3023IADG](/sequence-files/IGVFFI3023IADG/), [IGVFFI5028NMRQ](/sequence-files/IGVFFI5028NMRQ/), [IGVFFI8407ITWC](/sequence-files/IGVFFI8407ITWC/), [IGVFFI9645XCVK](/sequence-files/IGVFFI9645XCVK/), [IGVFFI8274RCDL](/sequence-files/IGVFFI8274RCDL/), [IGVFFI9218PNOW](/sequence-files/IGVFFI9218PNOW/), [IGVFFI2005BVXR](/sequence-files/IGVFFI2005BVXR/), [IGVFFI0336YUDX](/sequence-files/IGVFFI0336YUDX/), [IGVFFI9556RRAS](/sequence-files/IGVFFI9556RRAS/), [IGVFFI8109GRTZ](/sequence-files/IGVFFI8109GRTZ/), [IGVFFI3787SUKX](/sequence-files/IGVFFI3787SUKX/), [IGVFFI0298UZTN](/sequence-files/IGVFFI0298UZTN/), [IGVFFI2967HIMC](/sequence-files/IGVFFI2967HIMC/), [IGVFFI7814NTRF](/sequence-files/IGVFFI7814NTRF/), [IGVFFI8135RFIM](/sequence-files/IGVFFI8135RFIM/), [IGVFFI3507AKOR](/sequence-files/IGVFFI3507AKOR/), [IGVFFI7361RQNM](/sequence-files/IGVFFI7361RQNM/), [IGVFFI7320UZZR](/sequence-files/IGVFFI7320UZZR/), [IGVFFI4954PDLZ](/sequence-files/IGVFFI4954PDLZ/), [IGVFFI5733QAYX](/sequence-files/IGVFFI5733QAYX/), [IGVFFI0272CSIG](/sequence-files/IGVFFI0272CSIG/), [IGVFFI6376WPOX](/sequence-files/IGVFFI6376WPOX/), [IGVFFI0490BKQH](/sequence-files/IGVFFI0490BKQH/), [IGVFFI3330RGOP](/sequence-files/IGVFFI3330RGOP/), [IGVFFI2402DALV](/sequence-files/IGVFFI2402DALV/), [IGVFFI8436BPDB](/sequence-files/IGVFFI8436BPDB/), [IGVFFI6635RIMN](/sequence-files/IGVFFI6635RIMN/), [IGVFFI0471IVPR](/sequence-files/IGVFFI0471IVPR/), [IGVFFI4940IMMC](/sequence-files/IGVFFI4940IMMC/), [IGVFFI2882JCQF](/sequence-files/IGVFFI2882JCQF/), [IGVFFI2899VBFQ](/sequence-files/IGVFFI2899VBFQ/), [IGVFFI8605YTKP](/sequence-files/IGVFFI8605YTKP/), [IGVFFI8333OEQM](/sequence-files/IGVFFI8333OEQM/), [IGVFFI8714DXDX](/sequence-files/IGVFFI8714DXDX/), [IGVFFI3403QFJI](/sequence-files/IGVFFI3403QFJI/), [IGVFFI5202WMUP](/sequence-files/IGVFFI5202WMUP/), [IGVFFI3520AKLX](/sequence-files/IGVFFI3520AKLX/), [IGVFFI1185UUCQ](/sequence-files/IGVFFI1185UUCQ/), [IGVFFI9622KZUG](/sequence-files/IGVFFI9622KZUG/), [IGVFFI4672DBLB](/sequence-files/IGVFFI4672DBLB/), [IGVFFI2416RFQR](/sequence-files/IGVFFI2416RFQR/), [IGVFFI8156KCLN](/sequence-files/IGVFFI8156KCLN/), [IGVFFI4593MEQL](/sequence-files/IGVFFI4593MEQL/), [IGVFFI4617QJIC](/sequence-files/IGVFFI4617QJIC/) 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/IGVFDS7312BCBZ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7312BCBZ](/measurement-sets/IGVFDS7312BCBZ/) has sequence file(s): [IGVFFI7241XKKE](/sequence-files/IGVFFI7241XKKE/), [IGVFFI2087UMAQ](/sequence-files/IGVFFI2087UMAQ/), [IGVFFI9557VBNH](/sequence-files/IGVFFI9557VBNH/), [IGVFFI1419ZYLP](/sequence-files/IGVFFI1419ZYLP/), [IGVFFI3023IADG](/sequence-files/IGVFFI3023IADG/), [IGVFFI5028NMRQ](/sequence-files/IGVFFI5028NMRQ/), [IGVFFI8407ITWC](/sequence-files/IGVFFI8407ITWC/), [IGVFFI9645XCVK](/sequence-files/IGVFFI9645XCVK/), [IGVFFI8274RCDL](/sequence-files/IGVFFI8274RCDL/), [IGVFFI9218PNOW](/sequence-files/IGVFFI9218PNOW/), [IGVFFI2005BVXR](/sequence-files/IGVFFI2005BVXR/), [IGVFFI0336YUDX](/sequence-files/IGVFFI0336YUDX/), [IGVFFI9556RRAS](/sequence-files/IGVFFI9556RRAS/), [IGVFFI8109GRTZ](/sequence-files/IGVFFI8109GRTZ/), [IGVFFI3787SUKX](/sequence-files/IGVFFI3787SUKX/), [IGVFFI0298UZTN](/sequence-files/IGVFFI0298UZTN/), [IGVFFI2967HIMC](/sequence-files/IGVFFI2967HIMC/), [IGVFFI7814NTRF](/sequence-files/IGVFFI7814NTRF/), [IGVFFI8135RFIM](/sequence-files/IGVFFI8135RFIM/), [IGVFFI3507AKOR](/sequence-files/IGVFFI3507AKOR/), [IGVFFI7361RQNM](/sequence-files/IGVFFI7361RQNM/), [IGVFFI7320UZZR](/sequence-files/IGVFFI7320UZZR/), [IGVFFI4954PDLZ](/sequence-files/IGVFFI4954PDLZ/), [IGVFFI5733QAYX](/sequence-files/IGVFFI5733QAYX/), [IGVFFI0272CSIG](/sequence-files/IGVFFI0272CSIG/), [IGVFFI6376WPOX](/sequence-files/IGVFFI6376WPOX/), [IGVFFI0490BKQH](/sequence-files/IGVFFI0490BKQH/), [IGVFFI3330RGOP](/sequence-files/IGVFFI3330RGOP/), [IGVFFI2402DALV](/sequence-files/IGVFFI2402DALV/), [IGVFFI8436BPDB](/sequence-files/IGVFFI8436BPDB/), [IGVFFI6635RIMN](/sequence-files/IGVFFI6635RIMN/), [IGVFFI0471IVPR](/sequence-files/IGVFFI0471IVPR/), [IGVFFI4940IMMC](/sequence-files/IGVFFI4940IMMC/), [IGVFFI2882JCQF](/sequence-files/IGVFFI2882JCQF/), [IGVFFI2899VBFQ](/sequence-files/IGVFFI2899VBFQ/), [IGVFFI8605YTKP](/sequence-files/IGVFFI8605YTKP/), [IGVFFI8333OEQM](/sequence-files/IGVFFI8333OEQM/), [IGVFFI8714DXDX](/sequence-files/IGVFFI8714DXDX/), [IGVFFI3403QFJI](/sequence-files/IGVFFI3403QFJI/), [IGVFFI5202WMUP](/sequence-files/IGVFFI5202WMUP/), [IGVFFI3520AKLX](/sequence-files/IGVFFI3520AKLX/), [IGVFFI1185UUCQ](/sequence-files/IGVFFI1185UUCQ/), [IGVFFI9622KZUG](/sequence-files/IGVFFI9622KZUG/), [IGVFFI4672DBLB](/sequence-files/IGVFFI4672DBLB/), [IGVFFI2416RFQR](/sequence-files/IGVFFI2416RFQR/), [IGVFFI8156KCLN](/sequence-files/IGVFFI8156KCLN/), [IGVFFI4593MEQL](/sequence-files/IGVFFI4593MEQL/), [IGVFFI4617QJIC](/sequence-files/IGVFFI4617QJIC/) 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/IGVFDS7312BCBZ/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7312BCBZ](/measurement-sets/IGVFDS7312BCBZ/) 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/IGVFDS7312BCBZ/"
            }
        ]
    },
    "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": "2024-11-25T23:54:17.881691+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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            "content_type": "reads",
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        },
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            "@id": "/sequence-files/IGVFFI9557VBNH/",
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI9218PNOW/",
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            "aliases": [
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            ],
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            "upload_status": "validated"
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                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinC-PCRrep9_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:02:05.439470+00:00",
            "file_format": "fastq",
            "file_size": 6967509,
            "href": "/sequence-files/IGVFFI4593MEQL/@@download/IGVFFI4593MEQL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/09db8aa1-49ae-44de-a4df-648b0bfbab57/IGVFFI4593MEQL.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-BioRep2-FFrep3-BinC-PCRrep9_S735_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4617QJIC/",
            "accession": "IGVFFI4617QJIC",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-BinC-PCRrep5_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:52:31.446853+00:00",
            "file_format": "fastq",
            "file_size": 6907733,
            "href": "/sequence-files/IGVFFI4617QJIC/@@download/IGVFFI4617QJIC.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/faa3a459-7629-4f93-b2ac-f270540e648d/IGVFFI4617QJIC.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-BioRep2-FFrep3-BinC-PCRrep5_S731_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/IGVFSM7348HFRO/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7348HFRO",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep3-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": "2024-11-26T07:41:34.825314+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": "58087f62-a479-49f2-9b3a-46e2ab3fc0f8"
}