IGVFDS5266OEKB

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5266OEKB/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5266OEKB",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-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 [IGVFDS5266OEKB](/measurement-sets/IGVFDS5266OEKB/) has sequence file(s) [IGVFFI7280YNBF](/sequence-files/IGVFFI7280YNBF/), [IGVFFI7158ICFK](/sequence-files/IGVFFI7158ICFK/), [IGVFFI8289AMHK](/sequence-files/IGVFFI8289AMHK/), [IGVFFI0462XFML](/sequence-files/IGVFFI0462XFML/), [IGVFFI1736KRSA](/sequence-files/IGVFFI1736KRSA/), [IGVFFI2921FVWJ](/sequence-files/IGVFFI2921FVWJ/), [IGVFFI1555SXFN](/sequence-files/IGVFFI1555SXFN/), [IGVFFI9691LWUF](/sequence-files/IGVFFI9691LWUF/) 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/IGVFDS5266OEKB/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS5266OEKB](/measurement-sets/IGVFDS5266OEKB/) has sequence file(s): [IGVFFI7280YNBF](/sequence-files/IGVFFI7280YNBF/), [IGVFFI7158ICFK](/sequence-files/IGVFFI7158ICFK/), [IGVFFI8289AMHK](/sequence-files/IGVFFI8289AMHK/), [IGVFFI0462XFML](/sequence-files/IGVFFI0462XFML/), [IGVFFI1736KRSA](/sequence-files/IGVFFI1736KRSA/), [IGVFFI2921FVWJ](/sequence-files/IGVFFI2921FVWJ/), [IGVFFI1555SXFN](/sequence-files/IGVFFI1555SXFN/), [IGVFFI9691LWUF](/sequence-files/IGVFFI9691LWUF/) 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/IGVFDS5266OEKB/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5266OEKB](/measurement-sets/IGVFDS5266OEKB/) 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/IGVFDS5266OEKB/"
            }
        ]
    },
    "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": "2024-11-25T23:52:59.040645+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/IGVFFI7280YNBF/",
            "accession": "IGVFFI7280YNBF",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T06:43:20.143168+00:00",
            "file_format": "fastq",
            "file_size": 9483254,
            "href": "/sequence-files/IGVFFI7280YNBF/@@download/IGVFFI7280YNBF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/c8fe1239-dc2e-4487-b638-632443f05ab5/IGVFFI7280YNBF.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-FFrep3-BinAll-PCRrep2_S810_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7158ICFK/",
            "accession": "IGVFFI7158ICFK",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T06:41:49.999060+00:00",
            "file_format": "fastq",
            "file_size": 9441369,
            "href": "/sequence-files/IGVFFI7158ICFK/@@download/IGVFFI7158ICFK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/85efb6a3-f9f8-4b9d-be5b-2fc52992e03d/IGVFFI7158ICFK.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-FFrep3-BinAll-PCRrep1_S801_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8289AMHK/",
            "accession": "IGVFFI8289AMHK",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T08:58:04.493160+00:00",
            "file_format": "fastq",
            "file_size": 11053693,
            "href": "/sequence-files/IGVFFI8289AMHK/@@download/IGVFFI8289AMHK.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/919552f0-9194-41e4-9cba-f9af5ccafaaf/IGVFFI8289AMHK.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-FFrep3-BinAll-PCRrep2_S810_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0462XFML/",
            "accession": "IGVFFI0462XFML",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T08:55:20.756705+00:00",
            "file_format": "fastq",
            "file_size": 11033671,
            "href": "/sequence-files/IGVFFI0462XFML/@@download/IGVFFI0462XFML.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/2d0b77d4-c46e-490a-b3a1-61221288c2bd/IGVFFI0462XFML.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-FFrep3-BinAll-PCRrep1_S801_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1736KRSA/",
            "accession": "IGVFFI1736KRSA",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T12:49:57.126057+00:00",
            "file_format": "fastq",
            "file_size": 4228773,
            "href": "/sequence-files/IGVFFI1736KRSA/@@download/IGVFFI1736KRSA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/ad2da140-0aeb-4313-b8a6-b96d00b616b2/IGVFFI1736KRSA.fastq.gz",
            "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-FFrep3-BinAll-PCRrep2_S810_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2921FVWJ/",
            "accession": "IGVFFI2921FVWJ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T12:47:13.419041+00:00",
            "file_format": "fastq",
            "file_size": 3987095,
            "href": "/sequence-files/IGVFFI2921FVWJ/@@download/IGVFFI2921FVWJ.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/768a1912-17d1-4a4c-81ce-be1960e3124c/IGVFFI2921FVWJ.fastq.gz",
            "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-FFrep3-BinAll-PCRrep1_S801_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1555SXFN/",
            "accession": "IGVFFI1555SXFN",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T16:47:14.209391+00:00",
            "file_format": "fastq",
            "file_size": 4023760,
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            "s3_uri": "s3://igvf-files/2024/11/26/1ce0644a-7b83-4d5c-b292-46c9290c59e7/IGVFFI1555SXFN.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-FFrep3-BinAll-PCRrep2_S810_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9691LWUF/",
            "accession": "IGVFFI9691LWUF",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-FACS_Input-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T16:44:26.429197+00:00",
            "file_format": "fastq",
            "file_size": 4086867,
            "href": "/sequence-files/IGVFFI9691LWUF/@@download/IGVFFI9691LWUF.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/5def0af7-1403-44d4-bbca-a8316980f52e/IGVFFI9691LWUF.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-FFrep3-BinAll-PCRrep1_S801_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/IGVFSM9235XIKR/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9235XIKR",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep1-FFrep3-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": "2024-11-26T06:41:49.999060+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": "680b25c5-b695-491c-9758-98f65c4ca98b"
}