IGVFDS7859TASD

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7859TASD/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7859TASD",
    "aliases": [
        "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-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 [IGVFDS7859TASD](/measurement-sets/IGVFDS7859TASD/) has sequence file(s) [IGVFFI1619FDED](/sequence-files/IGVFFI1619FDED/), [IGVFFI4290XIZD](/sequence-files/IGVFFI4290XIZD/), [IGVFFI8923SAQP](/sequence-files/IGVFFI8923SAQP/), [IGVFFI2836ZXQS](/sequence-files/IGVFFI2836ZXQS/), [IGVFFI1713BHRU](/sequence-files/IGVFFI1713BHRU/), [IGVFFI2168LTUH](/sequence-files/IGVFFI2168LTUH/), [IGVFFI4650XMXL](/sequence-files/IGVFFI4650XMXL/), [IGVFFI6301PNSH](/sequence-files/IGVFFI6301PNSH/) 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/IGVFDS7859TASD/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7859TASD](/measurement-sets/IGVFDS7859TASD/) has sequence file(s): [IGVFFI1619FDED](/sequence-files/IGVFFI1619FDED/), [IGVFFI4290XIZD](/sequence-files/IGVFFI4290XIZD/), [IGVFFI8923SAQP](/sequence-files/IGVFFI8923SAQP/), [IGVFFI2836ZXQS](/sequence-files/IGVFFI2836ZXQS/), [IGVFFI1713BHRU](/sequence-files/IGVFFI1713BHRU/), [IGVFFI2168LTUH](/sequence-files/IGVFFI2168LTUH/), [IGVFFI4650XMXL](/sequence-files/IGVFFI4650XMXL/), [IGVFFI6301PNSH](/sequence-files/IGVFFI6301PNSH/) 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/IGVFDS7859TASD/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7859TASD](/measurement-sets/IGVFDS7859TASD/) 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/IGVFDS7859TASD/"
            }
        ]
    },
    "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/IGVFDS8210FQOO/",
            "accession": "IGVFDS8210FQOO",
            "aliases": [
                "jesse-engreitz:THP1-PE2_Exp7_PPIF_5SpliceSite-IndividualVariantExp_NegControl_AmpliconSequencing"
            ],
            "status": "preview"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2024-12-10T22:37:31.480142+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/IGVFFI1619FDED/",
            "accession": "IGVFFI1619FDED",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-10T23:49:05.545963+00:00",
            "file_format": "fastq",
            "file_size": 34820644,
            "href": "/sequence-files/IGVFFI1619FDED/@@download/IGVFFI1619FDED.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/10/1ac65dc1-bf53-49cd-bdd7-87ed3046964e/IGVFFI1619FDED.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4290XIZD/",
            "accession": "IGVFFI4290XIZD",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-10T23:52:05.567094+00:00",
            "file_format": "fastq",
            "file_size": 38575289,
            "href": "/sequence-files/IGVFFI4290XIZD/@@download/IGVFFI4290XIZD.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/10/b2b59b4c-56eb-4f94-a3d7-4dc47a96ef4e/IGVFFI4290XIZD.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8923SAQP/",
            "accession": "IGVFFI8923SAQP",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T16:57:32.089196+00:00",
            "file_format": "fastq",
            "file_size": 33158019,
            "href": "/sequence-files/IGVFFI8923SAQP/@@download/IGVFFI8923SAQP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/2a6418ae-d70a-4d7a-ac0f-d6d72d9fae09/IGVFFI8923SAQP.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2836ZXQS/",
            "accession": "IGVFFI2836ZXQS",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T16:56:02.096509+00:00",
            "file_format": "fastq",
            "file_size": 29966551,
            "href": "/sequence-files/IGVFFI2836ZXQS/@@download/IGVFFI2836ZXQS.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/9620da2a-d15d-4bbc-b6e4-6fc2cabe3ede/IGVFFI2836ZXQS.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1713BHRU/",
            "accession": "IGVFFI1713BHRU",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T20:33:38.802316+00:00",
            "file_format": "fastq",
            "file_size": 13517256,
            "href": "/sequence-files/IGVFFI1713BHRU/@@download/IGVFFI1713BHRU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/91d39c16-9012-4807-8bb4-8fcb83109bba/IGVFFI1713BHRU.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2168LTUH/",
            "accession": "IGVFFI2168LTUH",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T20:30:44.884510+00:00",
            "file_format": "fastq",
            "file_size": 11983735,
            "href": "/sequence-files/IGVFFI2168LTUH/@@download/IGVFFI2168LTUH.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/198e2932-42c7-486b-9f8c-cd6cf81ea667/IGVFFI2168LTUH.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4650XMXL/",
            "accession": "IGVFFI4650XMXL",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T22:46:17.194947+00:00",
            "file_format": "fastq",
            "file_size": 12730371,
            "href": "/sequence-files/IGVFFI4650XMXL/@@download/IGVFFI4650XMXL.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/54d3b289-8eae-48e3-b1a6-b6541d938ed2/IGVFFI4650XMXL.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0022840/",
                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S979_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6301PNSH/",
            "accession": "IGVFFI6301PNSH",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T22:43:15.692169+00:00",
            "file_format": "fastq",
            "file_size": 11310049,
            "href": "/sequence-files/IGVFFI6301PNSH/@@download/IGVFFI6301PNSH.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": "240908-S029-5splice-THP1-5splicesite_C10-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S967_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS8267JJHO/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "preferred_assay_title": "Variant-EFFECTS",
    "protocols": [
        "https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1"
    ],
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2894EXAV/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2894EXAV",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_TCCA-THP1-BioRep1-FFrep1-FACS_Input"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS9097TEUZ/",
                    "accession": "IGVFDS9097TEUZ",
                    "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": "2024-12-10T23:49:05.545963+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": "34365588-066c-4d4e-9bef-9ca60f52cf1e"
}