IGVFFI1055BRCU

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI1055BRCU/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI1055BRCU",
    "aliases": [
        "jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinD-PCRrep2_R2"
    ],
    "assay_titles": [
        "Variant FlowFISH"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released sequence file [IGVFFI1055BRCU](/sequence-files/IGVFFI1055BRCU/) has in progress subobject auxiliary set [IGVFDS9517URQU](/auxiliary-sets/IGVFDS9517URQU/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/sequence-files/IGVFFI1055BRCU/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG011972/",
        "component": "functional characterization"
    },
    "content_md5sum": "79aed06c8ceedf8a64036cf2ea97b5b3",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2023-12-05T20:18:03.747922+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS9517URQU/",
        "accession": "IGVFDS9517URQU",
        "file_set_type": "variant sequencing",
        "samples": [
            {
                "@id": "/in-vitro-systems/IGVFSM4844JJJX/",
                "accession": "IGVFSM4844JJJX",
                "classifications": [
                    "cell line"
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/EFO_0002796/",
                        "term_name": "Jurkat"
                    }
                ],
                "summary": "Jurkat cell line, male, Homo sapiens (sorting details: FACS bin for 55-65% expression of PPIF) treated with 100 ng/mL phorbol 13-acetate 12-myristate for 4 hours, 5 μg/mL T-cell surface glycoprotein CD3 gamma chain for 4 hours, modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transfected with a guide library",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "variant sequencing for prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus"
    },
    "file_size": 14571209,
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI1055BRCU/@@download/IGVFFI1055BRCU.fastq.gz",
    "illumina_read_type": "R2",
    "index": "CCTACCAT:ACTG",
    "input_file_for": [],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/jesse-engreitz/",
        "title": "Jesse Engreitz, Stanford"
    },
    "loci_list_for": [],
    "maximum_read_length": 150,
    "md5sum": "8f8c05b78cd437d061c4072aa578c2a0",
    "mean_read_length": 150,
    "minimum_read_length": 150,
    "read_count": 407132,
    "release_timestamp": "2023-12-21T00:12:09.250738+00:00",
    "s3_uri": "s3://igvf-files/2023/12/05/ff5aa3f3-b6b3-49d1-9067-0d2ddcc64388/IGVFFI1055BRCU.fastq.gz",
    "schema_version": "14",
    "seqspecs": [],
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008566/",
        "term_name": "Illumina NextSeq 550"
    },
    "sequencing_run": 1,
    "status": "released",
    "submitted_by": {
        "@id": "/users/f9e7cd82-a407-4a20-89ee-f4dc668b0cbe/",
        "title": "Michael Montgomery"
    },
    "submitted_file_name": "220829_pPPIF_JurkatVFF-Jurkat-PE2A-BFP-pPPIF-Amp_pPPIF2_S18-BioRep3-FFRep2-BinD-PCRrep2_S208_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 1",
    "upload_status": "validated",
    "uuid": "ff5aa3f3-b6b3-49d1-9067-0d2ddcc64388"
}