IGVFDS7024RXFA

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7024RXFA/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7024RXFA",
    "aliases": [
        "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-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 [IGVFDS7024RXFA](/measurement-sets/IGVFDS7024RXFA/) has sequence file(s) [IGVFFI2400TQJA](/sequence-files/IGVFFI2400TQJA/), [IGVFFI4320FLGE](/sequence-files/IGVFFI4320FLGE/), [IGVFFI9495EOET](/sequence-files/IGVFFI9495EOET/), [IGVFFI7117XVVN](/sequence-files/IGVFFI7117XVVN/), [IGVFFI5832HUGJ](/sequence-files/IGVFFI5832HUGJ/), [IGVFFI4183UTPP](/sequence-files/IGVFFI4183UTPP/), [IGVFFI8254XUFD](/sequence-files/IGVFFI8254XUFD/), [IGVFFI5277NQDZ](/sequence-files/IGVFFI5277NQDZ/) 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/IGVFDS7024RXFA/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7024RXFA](/measurement-sets/IGVFDS7024RXFA/) has sequence file(s): [IGVFFI2400TQJA](/sequence-files/IGVFFI2400TQJA/), [IGVFFI4320FLGE](/sequence-files/IGVFFI4320FLGE/), [IGVFFI9495EOET](/sequence-files/IGVFFI9495EOET/), [IGVFFI7117XVVN](/sequence-files/IGVFFI7117XVVN/), [IGVFFI5832HUGJ](/sequence-files/IGVFFI5832HUGJ/), [IGVFFI4183UTPP](/sequence-files/IGVFFI4183UTPP/), [IGVFFI8254XUFD](/sequence-files/IGVFFI8254XUFD/), [IGVFFI5277NQDZ](/sequence-files/IGVFFI5277NQDZ/) 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/IGVFDS7024RXFA/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7024RXFA](/measurement-sets/IGVFDS7024RXFA/) 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/IGVFDS7024RXFA/"
            }
        ]
    },
    "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": "2024-11-25T23:54:03.263620+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/IGVFFI2400TQJA/",
            "accession": "IGVFFI2400TQJA",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:28:19.430091+00:00",
            "file_format": "fastq",
            "file_size": 10048288,
            "href": "/sequence-files/IGVFFI2400TQJA/@@download/IGVFFI2400TQJA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/6f21729f-194c-496a-a033-ea5246e8b7ca/IGVFFI2400TQJA.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-FFrep2-BinAll-PCRrep2_S813_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4320FLGE/",
            "accession": "IGVFFI4320FLGE",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T07:26:39.890341+00:00",
            "file_format": "fastq",
            "file_size": 10337413,
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            "s3_uri": "s3://igvf-files/2024/11/26/01ead957-81f2-45a3-8988-c4479d9f8a47/IGVFFI4320FLGE.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-FFrep2-BinAll-PCRrep1_S804_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9495EOET/",
            "accession": "IGVFFI9495EOET",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T10:22:23.570134+00:00",
            "file_format": "fastq",
            "file_size": 11938228,
            "href": "/sequence-files/IGVFFI9495EOET/@@download/IGVFFI9495EOET.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/1632fc44-5035-4c5d-8246-2f8f2bcffcc0/IGVFFI9495EOET.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-FFrep2-BinAll-PCRrep1_S804_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7117XVVN/",
            "accession": "IGVFFI7117XVVN",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T10:25:18.916261+00:00",
            "file_format": "fastq",
            "file_size": 11887547,
            "href": "/sequence-files/IGVFFI7117XVVN/@@download/IGVFFI7117XVVN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/11/26/3e5dac1e-2119-430f-9b90-224491761556/IGVFFI7117XVVN.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-FFrep2-BinAll-PCRrep2_S813_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5832HUGJ/",
            "accession": "IGVFFI5832HUGJ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T14:15:41.017560+00:00",
            "file_format": "fastq",
            "file_size": 4560677,
            "href": "/sequence-files/IGVFFI5832HUGJ/@@download/IGVFFI5832HUGJ.fastq.gz",
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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-BioRep2-FFrep2-BinAll-PCRrep1_S804_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4183UTPP/",
            "accession": "IGVFFI4183UTPP",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T14:18:27.532099+00:00",
            "file_format": "fastq",
            "file_size": 4423865,
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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-BioRep2-FFrep2-BinAll-PCRrep2_S813_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8254XUFD/",
            "accession": "IGVFFI8254XUFD",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:14:17.365811+00:00",
            "file_format": "fastq",
            "file_size": 4378963,
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            "s3_uri": "s3://igvf-files/2024/11/26/5e5d4714-2694-4b56-9993-5e8cfcba8de1/IGVFFI8254XUFD.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-FFrep2-BinAll-PCRrep1_S804_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5277NQDZ/",
            "accession": "IGVFFI5277NQDZ",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-11-26T18:17:05.389018+00:00",
            "file_format": "fastq",
            "file_size": 4347590,
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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-FFrep2-BinAll-PCRrep2_S813_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/IGVFSM9480RXDI/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9480RXDI",
            "aliases": [
                "jesse-engreitz:240426S024-PPIFenhancervalidation-THP1_Amp_PPIF_enhancer-BioRep2-FFrep2-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": "2024-11-26T07:26:39.890341+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": "5d038a80-0efd-435a-99d5-0681d613874f"
}