IGVFDS7615TALZ

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7615TALZ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7615TALZ",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE_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 [IGVFSM8221MKMD](/in-vitro-systems/IGVFSM8221MKMD/) has in progress subobject construct library set [IGVFDS6377KNCH](/construct-library-sets/IGVFDS6377KNCH/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/in-vitro-systems/IGVFSM8221MKMD/"
            },
            {
                "category": "missing sequencing kit",
                "detail": "Measurement set [IGVFDS7615TALZ](/measurement-sets/IGVFDS7615TALZ/) has sequence file(s) [IGVFFI1817KLHC](/sequence-files/IGVFFI1817KLHC/), [IGVFFI8173DFJI](/sequence-files/IGVFFI8173DFJI/), [IGVFFI3374PNLH](/sequence-files/IGVFFI3374PNLH/), [IGVFFI8117RKCN](/sequence-files/IGVFFI8117RKCN/), [IGVFFI4261TCEU](/sequence-files/IGVFFI4261TCEU/), [IGVFFI1965BSVQ](/sequence-files/IGVFFI1965BSVQ/), [IGVFFI0654UCFO](/sequence-files/IGVFFI0654UCFO/), [IGVFFI5538UAFA](/sequence-files/IGVFFI5538UAFA/) 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/IGVFDS7615TALZ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7615TALZ](/measurement-sets/IGVFDS7615TALZ/) has sequence file(s): [IGVFFI1817KLHC](/sequence-files/IGVFFI1817KLHC/), [IGVFFI8173DFJI](/sequence-files/IGVFFI8173DFJI/), [IGVFFI3374PNLH](/sequence-files/IGVFFI3374PNLH/), [IGVFFI8117RKCN](/sequence-files/IGVFFI8117RKCN/), [IGVFFI4261TCEU](/sequence-files/IGVFFI4261TCEU/), [IGVFFI1965BSVQ](/sequence-files/IGVFFI1965BSVQ/), [IGVFFI0654UCFO](/sequence-files/IGVFFI0654UCFO/), [IGVFFI5538UAFA](/sequence-files/IGVFFI5538UAFA/) 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/IGVFDS7615TALZ/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7615TALZ](/measurement-sets/IGVFDS7615TALZ/) 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/IGVFDS7615TALZ/"
            }
        ]
    },
    "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/IGVFDS9477ARWI/",
            "accession": "IGVFDS9477ARWI",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing",
                "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-Jurkat-PE2_Exp1_NegControl_AmpliconSequencing"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-12-01T00:02:56.127952+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1080XFGV/",
            "accession": "IGVFDO1080XFGV",
            "aliases": [
                "igvf:donor_of_Jurkat"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI1817KLHC/",
            "accession": "IGVFFI1817KLHC",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T18:40:27.955998+00:00",
            "file_format": "fastq",
            "file_size": 7615764,
            "href": "/sequence-files/IGVFFI1817KLHC/@@download/IGVFFI1817KLHC.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/5f80cecb-f822-46d5-bdef-a9f8c748aade/IGVFFI1817KLHC.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8173DFJI/",
            "accession": "IGVFFI8173DFJI",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:25:04.503347+00:00",
            "file_format": "fastq",
            "file_size": 3081630,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3374PNLH/",
            "accession": "IGVFFI3374PNLH",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:12:28.397773+00:00",
            "file_format": "fastq",
            "file_size": 3160481,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI8117RKCN/",
            "accession": "IGVFFI8117RKCN",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T18:46:47.029156+00:00",
            "file_format": "fastq",
            "file_size": 7464041,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4261TCEU/",
            "accession": "IGVFFI4261TCEU",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:06:15.054496+00:00",
            "file_format": "fastq",
            "file_size": 3243011,
            "href": "/sequence-files/IGVFFI4261TCEU/@@download/IGVFFI4261TCEU.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/12/05/38dcc812-0d2d-4e30-b3a4-c5c08e31979f/IGVFFI4261TCEU.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI1965BSVQ/",
            "accession": "IGVFFI1965BSVQ",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T18:59:39.429238+00:00",
            "file_format": "fastq",
            "file_size": 13687953,
            "href": "/sequence-files/IGVFFI1965BSVQ/@@download/IGVFFI1965BSVQ.fastq.gz",
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep2_S61_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI0654UCFO/",
            "accession": "IGVFFI0654UCFO",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T19:18:43.376217+00:00",
            "file_format": "fastq",
            "file_size": 3124469,
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            "s3_uri": "s3://igvf-files/2023/12/05/24a6275e-efa9-4a39-835b-7fce4e469cfc/IGVFFI0654UCFO.fastq.gz",
            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI5538UAFA/",
            "accession": "IGVFFI5538UAFA",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-12-05T18:53:06.781506+00:00",
            "file_format": "fastq",
            "file_size": 13913385,
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            "sequencing_platform": {
                "@id": "/platform-terms/EFO_0008566/",
                "status": "released",
                "term_name": "Illumina NextSeq 550"
            },
            "status": "released",
            "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF_S2-BioRep1-FFRep1-BinE-PCRrep1_S5_R2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS9162RHFP/"
    ],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "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": "2023-12-20T23:04:32.071369+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM8221MKMD/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM8221MKMD",
            "aliases": [
                "jesse-engreitz:220829_8merInsertion-Jurkat_NoStimulation-Amp_PPIF_promoter-BioRep1-FFrep1-BinE"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS6377KNCH/",
                    "accession": "IGVFDS6377KNCH",
                    "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_0002796/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:Jurkat"
                    ],
                    "status": "released",
                    "summary": "Jurkat",
                    "term_name": "Jurkat"
                }
            ],
            "status": "released",
            "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 80-90% 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": "2023-12-05T18:40:27.955998+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": "19f6be30-87a4-4270-b270-ec15d026f67a"
}