IGVFDS7114WEPZ

{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS7114WEPZ/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7114WEPZ",
    "aliases": [
        "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-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 [IGVFDS7114WEPZ](/measurement-sets/IGVFDS7114WEPZ/) has sequence file(s) [IGVFFI4033OVLA](/sequence-files/IGVFFI4033OVLA/), [IGVFFI9739MMIU](/sequence-files/IGVFFI9739MMIU/), [IGVFFI3229MNJP](/sequence-files/IGVFFI3229MNJP/), [IGVFFI3547UHDU](/sequence-files/IGVFFI3547UHDU/), [IGVFFI9601YPAU](/sequence-files/IGVFFI9601YPAU/), [IGVFFI4789ELUN](/sequence-files/IGVFFI4789ELUN/), [IGVFFI7267CIMW](/sequence-files/IGVFFI7267CIMW/), [IGVFFI7423TDGE](/sequence-files/IGVFFI7423TDGE/) 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/IGVFDS7114WEPZ/"
            },
            {
                "category": "missing sequence specification",
                "detail": "Measurement set [IGVFDS7114WEPZ](/measurement-sets/IGVFDS7114WEPZ/) has sequence file(s): [IGVFFI4033OVLA](/sequence-files/IGVFFI4033OVLA/), [IGVFFI9739MMIU](/sequence-files/IGVFFI9739MMIU/), [IGVFFI3229MNJP](/sequence-files/IGVFFI3229MNJP/), [IGVFFI3547UHDU](/sequence-files/IGVFFI3547UHDU/), [IGVFFI9601YPAU](/sequence-files/IGVFFI9601YPAU/), [IGVFFI4789ELUN](/sequence-files/IGVFFI4789ELUN/), [IGVFFI7267CIMW](/sequence-files/IGVFFI7267CIMW/), [IGVFFI7423TDGE](/sequence-files/IGVFFI7423TDGE/) 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/IGVFDS7114WEPZ/"
            }
        ],
        "WARNING": [
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS7114WEPZ](/measurement-sets/IGVFDS7114WEPZ/) 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/IGVFDS7114WEPZ/"
            }
        ]
    },
    "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": "2024-12-10T22:32:05.019144+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/IGVFFI4033OVLA/",
            "accession": "IGVFFI4033OVLA",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T00:32:39.243527+00:00",
            "file_format": "fastq",
            "file_size": 35152200,
            "href": "/sequence-files/IGVFFI4033OVLA/@@download/IGVFFI4033OVLA.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/ea2f7548-0bd4-48a7-914a-6808e13092f3/IGVFFI4033OVLA.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9739MMIU/",
            "accession": "IGVFFI9739MMIU",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T00:35:55.059006+00:00",
            "file_format": "fastq",
            "file_size": 35682824,
            "href": "/sequence-files/IGVFFI9739MMIU/@@download/IGVFFI9739MMIU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/97311dc2-2aee-4fa0-a45f-b5a7dce08dc8/IGVFFI9739MMIU.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_R1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3229MNJP/",
            "accession": "IGVFFI3229MNJP",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T17:23:06.228534+00:00",
            "file_format": "fastq",
            "file_size": 30424923,
            "href": "/sequence-files/IGVFFI3229MNJP/@@download/IGVFFI3229MNJP.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/1197bac6-d386-45cb-a09f-316c6abbc156/IGVFFI3229MNJP.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI3547UHDU/",
            "accession": "IGVFFI3547UHDU",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_R2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T17:25:26.165381+00:00",
            "file_format": "fastq",
            "file_size": 30630241,
            "href": "/sequence-files/IGVFFI3547UHDU/@@download/IGVFFI3547UHDU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/a17f2f83-dbea-46f9-a6f0-4c7f134b9170/IGVFFI3547UHDU.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_R2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI9601YPAU/",
            "accession": "IGVFFI9601YPAU",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T23:30:40.852869+00:00",
            "file_format": "fastq",
            "file_size": 11743232,
            "href": "/sequence-files/IGVFFI9601YPAU/@@download/IGVFFI9601YPAU.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/cb38b091-f7a9-4561-ba9c-b2951c04adbd/IGVFFI9601YPAU.fastq.gz",
            "sequencing_platform": {
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                "status": "released",
                "term_name": "Illumina NovaSeq X"
            },
            "status": "preview",
            "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_I2_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI4789ELUN/",
            "accession": "IGVFFI4789ELUN",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T21:14:55.993092+00:00",
            "file_format": "fastq",
            "file_size": 11232458,
            "href": "/sequence-files/IGVFFI4789ELUN/@@download/IGVFFI4789ELUN.fastq.gz",
            "s3_uri": "s3://igvf-files/2024/12/11/944a56d2-af2f-47ba-a5a2-a80963361edf/IGVFFI4789ELUN.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7267CIMW/",
            "accession": "IGVFFI7267CIMW",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep2_I1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T21:17:56.706879+00:00",
            "file_format": "fastq",
            "file_size": 12939067,
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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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep2_S983_I1_001.fastq.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/sequence-files/IGVFFI7423TDGE/",
            "accession": "IGVFFI7423TDGE",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input-PCRrep1_I2"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2024-12-11T23:27:33.630126+00:00",
            "file_format": "fastq",
            "file_size": 11209754,
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            "s3_uri": "s3://igvf-files/2024/12/11/714077f8-a0d2-4ef2-9583-d9bea76469a1/IGVFFI7423TDGE.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_C11-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinAll-PCRrep1_S971_I2_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS1132MKHT/"
    ],
    "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/IGVFSM7040CAHB/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7040CAHB",
            "aliases": [
                "jesse-engreitz:240908-S029-PPIF_5SpliceSite-IndividualVariantExp-AGGT_CAAC-THP1-BioRep1-FFrep1-FACS_Input"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS2432IDGC/",
                    "accession": "IGVFDS2432IDGC",
                    "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": "2024-12-11T00:32:39.243527+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": "08a89adb-da54-401d-a8e0-9112ffc201b1"
}