IGVFFI3082ZUDE

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI3082ZUDE/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI3082ZUDE",
    "aliases": [
        "charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep2-R1"
    ],
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "7a70e99764479e1b6dc6a4ae7502c2c6",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2023-11-08T20:33:48.931892+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS9073AJJA/",
        "accession": "IGVFDS9073AJJA",
        "file_set_type": "gRNA sequencing",
        "samples": [
            {
                "@id": "/primary-cells/IGVFSM7634EVUP/",
                "accession": "IGVFSM7634EVUP",
                "classifications": [
                    "primary cell"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                        "modality": "activation",
                        "summary": "CRISPRa Sa-dCas9-VP64"
                    }
                ],
                "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 90-100% expression of CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes"
    },
    "file_size": 62381783,
    "flowcell_id": "000000000-K4RT4",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI3082ZUDE/@@download/IGVFFI3082ZUDE.fastq.gz",
    "illumina_read_type": "R1",
    "input_file_for": [
        "/alignment-files/IGVFFI5368ITLJ/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "lane": 1,
    "loci_list_for": [],
    "maximum_read_length": 22,
    "md5sum": "ecd523d7bee18ab926ae307a8799fadb",
    "mean_read_length": 22,
    "minimum_read_length": 22,
    "read_count": 2649829,
    "release_timestamp": "2024-11-18T21:08:53.096938+00:00",
    "s3_uri": "s3://igvf-files/2023/11/08/12396e8a-bd29-4adc-a687-c6e3303682d1/IGVFFI3082ZUDE.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/CCR7pos-pSM54-TF-H2_S8_L001_R1_001.fastq.gz",
    "summary": "R1 reads from sequencing run 2",
    "upload_status": "validated",
    "uuid": "12396e8a-bd29-4adc-a687-c6e3303682d1"
}