IGVFFI4013TWUP

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI4013TWUP/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI4013TWUP",
    "aliases": [
        "jesse-engreitz:240908-S029-PPIF_5SpliceSitePool-THP1-BioRep1-FFrep1-BinC-PCRrep4_R2"
    ],
    "assay_titles": [
        "Variant-EFFECTS"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "content_md5sum": "9bf45f08ce5c773cf0be2b2ebab46dcb",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2024-12-01T21:29:32.925874+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/measurement-sets/IGVFDS3800XFMC/",
        "accession": "IGVFDS3800XFMC",
        "file_set_type": "experimental data",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM5956MLVS/",
                "accession": "IGVFSM5956MLVS",
                "classifications": [
                    "cell line"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/fc6bc0b3-a064-47d0-b95d-a9af14bb1624/",
                        "modality": "prime editing",
                        "status": "released",
                        "summary": "CRISPR prime editing Sp-nCas9-M-MLV RT (PE2)"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0001253/",
                        "status": "released",
                        "term_name": "THP-1"
                    }
                ],
                "status": "preview",
                "summary": "THP-1 cell line, male, Homo sapiens (sorting details: FACS bin for 51-75% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
                "taxa": "Homo sapiens"
            }
        ],
        "status": "preview",
        "summary": "CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
    },
    "file_size": 11717664,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI4013TWUP/@@download/IGVFFI4013TWUP.fastq.gz",
    "illumina_read_type": "R2",
    "index": "CAGGAGCC:GATATCGA",
    "input_file_for": [
        "/tabular-files/IGVFFI1798XNPV/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "loci_list_for": [],
    "maximum_read_length": 151,
    "md5sum": "d9592ee9e33df4fb7e2c0161d2515f73",
    "mean_read_length": 151,
    "minimum_read_length": 151,
    "read_count": 604632,
    "s3_uri": "s3://igvf-files/2024/12/01/28d62753-71bd-4b45-9ace-9f3c72eca0da/IGVFFI4013TWUP.fastq.gz",
    "schema_version": "14",
    "seqspecs": [],
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0022840/",
        "status": "released",
        "term_name": "Illumina NovaSeq X"
    },
    "sequencing_run": 1,
    "status": "preview",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_file_name": "240908-S029-5splice-THP1-5splicesite_pool-Amp_PPIF_5splicesite-BioRep1-FFrep1-BinC-PCRrep4_S745_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "28d62753-71bd-4b45-9ace-9f3c72eca0da"
}