IGVFFI2908JEGF

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI2908JEGF/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI2908JEGF",
    "aliases": [
        "charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep2-R1"
    ],
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "c9b032526ffe05327465eb23d2abc399",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2023-11-08T20:30:23.967927+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS4170XDRQ/",
        "accession": "IGVFDS4170XDRQ",
        "file_set_type": "gRNA sequencing",
        "samples": [
            {
                "@id": "/primary-cells/IGVFSM7158ADKU/",
                "accession": "IGVFSM7158ADKU",
                "classifications": [
                    "primary cell"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
                        "modality": "knockout",
                        "summary": "CRISPRko Sp-Cas9"
                    }
                ],
                "sample_terms": [
                    {
                        "@id": "/sample-terms/CL_0000909/",
                        "term_name": "CD8-positive, alpha-beta memory T cell"
                    }
                ],
                "summary": "CD8-positive, alpha-beta memory T cell, Homo sapiens (sorting details: FACS bin for 0-10% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "gRNA sequencing for CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes"
    },
    "file_size": 642728147,
    "flowcell_id": "AACJJ7LM5",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI2908JEGF/@@download/IGVFFI2908JEGF.fastq.gz",
    "illumina_read_type": "R1",
    "input_file_for": [
        "/alignment-files/IGVFFI1995JCIO/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "lane": 1,
    "loci_list_for": [],
    "maximum_read_length": 21,
    "md5sum": "4cee922eb21483efc2def02e3fa6e56b",
    "mean_read_length": 21,
    "minimum_read_length": 21,
    "read_count": 40097828,
    "release_timestamp": "2024-11-18T21:09:01.458223+00:00",
    "s3_uri": "s3://igvf-files/2023/11/08/f1067ac7-08d9-41e8-a68e-e3562208f369/IGVFFI2908JEGF.fastq.gz",
    "schema_version": "14",
    "seqspecs": [],
    "sequencing_kit": "MiSeq Reagent Kit v2",
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0004205/",
        "term_name": "Illumina MiSeq"
    },
    "sequencing_run": 2,
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM74_L3_S9_L001_R1_001.fastq.gz",
    "summary": "R1 reads from sequencing run 2",
    "upload_status": "validated",
    "uuid": "f1067ac7-08d9-41e8-a68e-e3562208f369"
}