IGVFDS8356GTHO

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8356GTHO/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8356GTHO",
    "aliases": [
        "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD_AmpliconSequencing"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released in vitro system [IGVFSM9715TWHE](/in-vitro-systems/IGVFSM9715TWHE/) has in progress subobject construct library set [IGVFDS6982DESN](/construct-library-sets/IGVFDS6982DESN/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM9715TWHE/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS8356GTHO](/measurement-sets/IGVFDS8356GTHO/) has sequence file(s) [IGVFFI4785YHXU](/sequence-files/IGVFFI4785YHXU/), [IGVFFI4568GFTG](/sequence-files/IGVFFI4568GFTG/), [IGVFFI6530CELH](/sequence-files/IGVFFI6530CELH/), [IGVFFI1452CSHN](/sequence-files/IGVFFI1452CSHN/), [IGVFFI9114ALHR](/sequence-files/IGVFFI9114ALHR/), [IGVFFI1148TMWC](/sequence-files/IGVFFI1148TMWC/), [IGVFFI1565JNTM](/sequence-files/IGVFFI1565JNTM/), [IGVFFI5022BOGU](/sequence-files/IGVFFI5022BOGU/), [IGVFFI0467ULNZ](/sequence-files/IGVFFI0467ULNZ/), [IGVFFI9697JRCR](/sequence-files/IGVFFI9697JRCR/), [IGVFFI2513VZJW](/sequence-files/IGVFFI2513VZJW/), [IGVFFI6931LKTV](/sequence-files/IGVFFI6931LKTV/), [IGVFFI3157OMHJ](/sequence-files/IGVFFI3157OMHJ/), [IGVFFI0195KDJP](/sequence-files/IGVFFI0195KDJP/), [IGVFFI8177MYCI](/sequence-files/IGVFFI8177MYCI/), [IGVFFI0934INHF](/sequence-files/IGVFFI0934INHF/), [IGVFFI1899RVQH](/sequence-files/IGVFFI1899RVQH/), [IGVFFI0142NJLL](/sequence-files/IGVFFI0142NJLL/), [IGVFFI0265AZWF](/sequence-files/IGVFFI0265AZWF/), [IGVFFI6115UFLP](/sequence-files/IGVFFI6115UFLP/), [IGVFFI7897FQDS](/sequence-files/IGVFFI7897FQDS/), [IGVFFI6602PDFK](/sequence-files/IGVFFI6602PDFK/), [IGVFFI4593AFPG](/sequence-files/IGVFFI4593AFPG/), [IGVFFI5166OCPX](/sequence-files/IGVFFI5166OCPX/), [IGVFFI7743SDGS](/sequence-files/IGVFFI7743SDGS/), [IGVFFI9164YJYG](/sequence-files/IGVFFI9164YJYG/), [IGVFFI9961WQGA](/sequence-files/IGVFFI9961WQGA/), [IGVFFI0959UBMT](/sequence-files/IGVFFI0959UBMT/), [IGVFFI8163LYDI](/sequence-files/IGVFFI8163LYDI/), [IGVFFI9244ZVIG](/sequence-files/IGVFFI9244ZVIG/), [IGVFFI9579PKRX](/sequence-files/IGVFFI9579PKRX/), [IGVFFI6873EQWD](/sequence-files/IGVFFI6873EQWD/), [IGVFFI0669UVXO](/sequence-files/IGVFFI0669UVXO/), [IGVFFI6523BPLR](/sequence-files/IGVFFI6523BPLR/), [IGVFFI8534SVUL](/sequence-files/IGVFFI8534SVUL/), [IGVFFI8742CHFV](/sequence-files/IGVFFI8742CHFV/), [IGVFFI2703GDGR](/sequence-files/IGVFFI2703GDGR/), [IGVFFI8979BVWT](/sequence-files/IGVFFI8979BVWT/), [IGVFFI3311SHVZ](/sequence-files/IGVFFI3311SHVZ/), [IGVFFI2452QHHG](/sequence-files/IGVFFI2452QHHG/), [IGVFFI8982QDFT](/sequence-files/IGVFFI8982QDFT/), [IGVFFI8982WTIO](/sequence-files/IGVFFI8982WTIO/), [IGVFFI7401KWUE](/sequence-files/IGVFFI7401KWUE/), [IGVFFI0046QKFS](/sequence-files/IGVFFI0046QKFS/), [IGVFFI4012DQEV](/sequence-files/IGVFFI4012DQEV/), [IGVFFI2057GMQO](/sequence-files/IGVFFI2057GMQO/), [IGVFFI0925HJEU](/sequence-files/IGVFFI0925HJEU/), [IGVFFI4610VZCI](/sequence-files/IGVFFI4610VZCI/) 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/IGVFDS8356GTHO/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS8356GTHO](/measurement-sets/IGVFDS8356GTHO/) has sequence file(s): [IGVFFI4785YHXU](/sequence-files/IGVFFI4785YHXU/), [IGVFFI4568GFTG](/sequence-files/IGVFFI4568GFTG/), [IGVFFI6530CELH](/sequence-files/IGVFFI6530CELH/), [IGVFFI1452CSHN](/sequence-files/IGVFFI1452CSHN/), [IGVFFI9114ALHR](/sequence-files/IGVFFI9114ALHR/), [IGVFFI1148TMWC](/sequence-files/IGVFFI1148TMWC/), [IGVFFI1565JNTM](/sequence-files/IGVFFI1565JNTM/), [IGVFFI5022BOGU](/sequence-files/IGVFFI5022BOGU/), [IGVFFI0467ULNZ](/sequence-files/IGVFFI0467ULNZ/), [IGVFFI9697JRCR](/sequence-files/IGVFFI9697JRCR/), [IGVFFI2513VZJW](/sequence-files/IGVFFI2513VZJW/), [IGVFFI6931LKTV](/sequence-files/IGVFFI6931LKTV/), [IGVFFI3157OMHJ](/sequence-files/IGVFFI3157OMHJ/), [IGVFFI0195KDJP](/sequence-files/IGVFFI0195KDJP/), [IGVFFI8177MYCI](/sequence-files/IGVFFI8177MYCI/), [IGVFFI0934INHF](/sequence-files/IGVFFI0934INHF/), [IGVFFI1899RVQH](/sequence-files/IGVFFI1899RVQH/), [IGVFFI0142NJLL](/sequence-files/IGVFFI0142NJLL/), [IGVFFI0265AZWF](/sequence-files/IGVFFI0265AZWF/), [IGVFFI6115UFLP](/sequence-files/IGVFFI6115UFLP/), [IGVFFI7897FQDS](/sequence-files/IGVFFI7897FQDS/), [IGVFFI6602PDFK](/sequence-files/IGVFFI6602PDFK/), [IGVFFI4593AFPG](/sequence-files/IGVFFI4593AFPG/), [IGVFFI5166OCPX](/sequence-files/IGVFFI5166OCPX/), [IGVFFI7743SDGS](/sequence-files/IGVFFI7743SDGS/), [IGVFFI9164YJYG](/sequence-files/IGVFFI9164YJYG/), [IGVFFI9961WQGA](/sequence-files/IGVFFI9961WQGA/), [IGVFFI0959UBMT](/sequence-files/IGVFFI0959UBMT/), [IGVFFI8163LYDI](/sequence-files/IGVFFI8163LYDI/), [IGVFFI9244ZVIG](/sequence-files/IGVFFI9244ZVIG/), [IGVFFI9579PKRX](/sequence-files/IGVFFI9579PKRX/), [IGVFFI6873EQWD](/sequence-files/IGVFFI6873EQWD/), [IGVFFI0669UVXO](/sequence-files/IGVFFI0669UVXO/), [IGVFFI6523BPLR](/sequence-files/IGVFFI6523BPLR/), [IGVFFI8534SVUL](/sequence-files/IGVFFI8534SVUL/), [IGVFFI8742CHFV](/sequence-files/IGVFFI8742CHFV/), [IGVFFI2703GDGR](/sequence-files/IGVFFI2703GDGR/), [IGVFFI8979BVWT](/sequence-files/IGVFFI8979BVWT/), [IGVFFI3311SHVZ](/sequence-files/IGVFFI3311SHVZ/), [IGVFFI2452QHHG](/sequence-files/IGVFFI2452QHHG/), [IGVFFI8982QDFT](/sequence-files/IGVFFI8982QDFT/), [IGVFFI8982WTIO](/sequence-files/IGVFFI8982WTIO/), [IGVFFI7401KWUE](/sequence-files/IGVFFI7401KWUE/), [IGVFFI0046QKFS](/sequence-files/IGVFFI0046QKFS/), [IGVFFI4012DQEV](/sequence-files/IGVFFI4012DQEV/), [IGVFFI2057GMQO](/sequence-files/IGVFFI2057GMQO/), [IGVFFI0925HJEU](/sequence-files/IGVFFI0925HJEU/), [IGVFFI4610VZCI](/sequence-files/IGVFFI4610VZCI/) 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/IGVFDS8356GTHO/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS8356GTHO](/measurement-sets/IGVFDS8356GTHO/) 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/IGVFDS8356GTHO/"
            }
        ]
    },
    "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/IGVFDS5864UGFT/",
            "accession": "IGVFDS5864UGFT",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-THP1-PE2_Exp2_NegControl_AmpliconSequencing"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-12-01T00:05:36.165833+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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            "@id": "/sequence-files/IGVFFI4785YHXU/",
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            "controlled_access": false,
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                "status": "released",
                "term_name": "Illumina NextSeq 550"
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            "submitted_file_name": "230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep11_S47_R2_001.fastq.gz",
            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI4568GFTG/",
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                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep6_I1"
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI6530CELH/",
            "accession": "IGVFFI6530CELH",
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        },
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            "@id": "/sequence-files/IGVFFI1452CSHN/",
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        },
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            "upload_status": "validated"
        },
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            "@id": "/sequence-files/IGVFFI1148TMWC/",
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        },
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            "@id": "/sequence-files/IGVFFI1565JNTM/",
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        },
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            "@id": "/sequence-files/IGVFFI9697JRCR/",
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            ],
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            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI2513VZJW/",
            "accession": "IGVFFI2513VZJW",
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                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD-PCRrep5_I2"
            ],
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    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. 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"
    ],
    "release_timestamp": "2023-12-20T23:06:38.520594+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9715TWHE/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM9715TWHE",
            "aliases": [
                "jesse-engreitz:230807S022-THP1-P153-Amp_PPIF_promoter-BioRep1-FFrep1-BinD"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6982DESN/",
                    "accession": "IGVFDS6982DESN",
                    "file_set_type": "guide library",
                    "status": "in progress",
                    "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": "released",
            "summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 76-100% 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": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_files_timestamp": "2023-12-05T19:51:13.468743+00:00",
    "summary": "CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF 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": "f2163f4b-b67b-45d3-ab31-c5171b60b5ab"
}