IGVFDS0958ZMWD

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS0958ZMWD/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0958ZMWD",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input_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 [IGVFDS0958ZMWD](/measurement-sets/IGVFDS0958ZMWD/) has sequence file(s) [IGVFFI6577PXWB](/sequence-files/IGVFFI6577PXWB/), [IGVFFI5542SKQI](/sequence-files/IGVFFI5542SKQI/), [IGVFFI1327ALTG](/sequence-files/IGVFFI1327ALTG/), [IGVFFI3455BXOP](/sequence-files/IGVFFI3455BXOP/), [IGVFFI6723ELCL](/sequence-files/IGVFFI6723ELCL/), [IGVFFI5103PMSC](/sequence-files/IGVFFI5103PMSC/), [IGVFFI9584LEOX](/sequence-files/IGVFFI9584LEOX/), [IGVFFI8527QSHR](/sequence-files/IGVFFI8527QSHR/) 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/IGVFDS0958ZMWD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS0958ZMWD](/measurement-sets/IGVFDS0958ZMWD/) has sequence file(s): [IGVFFI6577PXWB](/sequence-files/IGVFFI6577PXWB/), [IGVFFI5542SKQI](/sequence-files/IGVFFI5542SKQI/), [IGVFFI1327ALTG](/sequence-files/IGVFFI1327ALTG/), [IGVFFI3455BXOP](/sequence-files/IGVFFI3455BXOP/), [IGVFFI6723ELCL](/sequence-files/IGVFFI6723ELCL/), [IGVFFI5103PMSC](/sequence-files/IGVFFI5103PMSC/), [IGVFFI9584LEOX](/sequence-files/IGVFFI9584LEOX/), [IGVFFI8527QSHR](/sequence-files/IGVFFI8527QSHR/) 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/IGVFDS0958ZMWD/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS0958ZMWD](/measurement-sets/IGVFDS0958ZMWD/) 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/IGVFDS0958ZMWD/"
            }
        ]
    },
    "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": "2024-11-25T23:54:47.098543+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": [
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            "@id": "/sequence-files/IGVFFI6577PXWB/",
            "accession": "IGVFFI6577PXWB",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:57:47.004850+00:00",
            "file_format": "fastq",
            "file_size": 10655757,
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            "s3_uri": "s3://igvf-files/2024/11/26/856d9299-f273-4257-ab4b-0e87fa012e0b/IGVFFI6577PXWB.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-FFrep4-BinAll-PCRrep1_S806_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5542SKQI/",
            "accession": "IGVFFI5542SKQI",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:59:23.285994+00:00",
            "file_format": "fastq",
            "file_size": 10910100,
            "href": "/sequence-files/IGVFFI5542SKQI/@@download/IGVFFI5542SKQI.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/ba204b63-6913-4e1d-b5b8-0fbc0e61b48b/IGVFFI5542SKQI.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-FFrep4-BinAll-PCRrep2_S815_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1327ALTG/",
            "accession": "IGVFFI1327ALTG",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T11:22:38.671754+00:00",
            "file_format": "fastq",
            "file_size": 12663890,
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            "s3_uri": "s3://igvf-files/2024/11/26/5eaad445-5b41-4828-b993-a233d466f0fc/IGVFFI1327ALTG.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-FFrep4-BinAll-PCRrep2_S815_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3455BXOP/",
            "accession": "IGVFFI3455BXOP",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T11:19:46.062074+00:00",
            "file_format": "fastq",
            "file_size": 12367700,
            "href": "/sequence-files/IGVFFI3455BXOP/@@download/IGVFFI3455BXOP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/9a400258-be9d-4d0c-ac17-f9b5a0c65c4b/IGVFFI3455BXOP.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-FFrep4-BinAll-PCRrep1_S806_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6723ELCL/",
            "accession": "IGVFFI6723ELCL",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T15:16:59.318939+00:00",
            "file_format": "fastq",
            "file_size": 4630670,
            "href": "/sequence-files/IGVFFI6723ELCL/@@download/IGVFFI6723ELCL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/7c7c32fb-fe7e-4e91-8ae3-9edf7bb94b64/IGVFFI6723ELCL.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-FFrep4-BinAll-PCRrep2_S815_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5103PMSC/",
            "accession": "IGVFFI5103PMSC",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T15:14:06.633098+00:00",
            "file_format": "fastq",
            "file_size": 4471489,
            "href": "/sequence-files/IGVFFI5103PMSC/@@download/IGVFFI5103PMSC.fastq.gz",
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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-BioRep2-FFrep4-BinAll-PCRrep1_S806_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9584LEOX/",
            "accession": "IGVFFI9584LEOX",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:12:50.921827+00:00",
            "file_format": "fastq",
            "file_size": 4504024,
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            "s3_uri": "s3://igvf-files/2024/11/26/1e7c8e47-8110-45d4-9194-b61bec03794a/IGVFFI9584LEOX.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-FFrep4-BinAll-PCRrep1_S806_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8527QSHR/",
            "accession": "IGVFFI8527QSHR",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T19:15:44.760403+00:00",
            "file_format": "fastq",
            "file_size": 4800479,
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            "s3_uri": "s3://igvf-files/2024/11/26/4f4238e5-c0b8-44f0-9985-a9f8b56ff1a2/IGVFFI8527QSHR.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-FFrep4-BinAll-PCRrep2_S815_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/IGVFSM2515ITJE/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2515ITJE",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input"
            ],
            "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 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": "2024-11-26T07:57:47.004850+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": "511f94e5-3ef3-4821-9f42-e2a84bfac406"
}