IGVFFI3652DBNT

{
    "@context": "/terms/",
    "@id": "/sequence-files/IGVFFI3652DBNT/",
    "@type": [
        "SequenceFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI3652DBNT",
    "aliases": [
        "charles-gersbach:cd8-tcells-perturb-seq-crispra-grna-rep3-rep3-fastq-lane3-R2"
    ],
    "assay_titles": [
        "Perturb-seq"
    ],
    "audit": {},
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "dc872eaf8d499a7b0588ef1eaff07d45",
    "content_type": "reads",
    "controlled_access": false,
    "creation_timestamp": "2023-11-09T19:41:51.283265+00:00",
    "externally_hosted": false,
    "file_format": "fastq",
    "file_set": {
        "@id": "/auxiliary-sets/IGVFDS3945FAEL/",
        "accession": "IGVFDS3945FAEL",
        "file_set_type": "gRNA sequencing",
        "samples": [
            {
                "@id": "/primary-cells/IGVFSM2105CLXS/",
                "accession": "IGVFSM2105CLXS",
                "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 modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "gRNA sequencing for activation Perturb-seq integrating a guide (sgRNA) library targeting transcription start sites in 24 genes"
    },
    "file_size": 2492268603,
    "flowcell_id": "HMCCWDSX3",
    "gene_list_for": [],
    "href": "/sequence-files/IGVFFI3652DBNT/@@download/IGVFFI3652DBNT.fastq.gz",
    "illumina_read_type": "R2",
    "input_file_for": [
        "/matrix-files/IGVFFI6124CLAF/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "lane": 3,
    "loci_list_for": [],
    "maximum_read_length": 90,
    "md5sum": "4c2528ea0d059d64438c9ddac220b7df",
    "mean_read_length": 90,
    "minimum_read_length": 90,
    "read_count": 65258100,
    "release_timestamp": "2024-10-18T19:49:56.763820+00:00",
    "s3_uri": "s3://igvf-files/2023/11/09/92f93e1d-90e7-403a-9b49-730fab6237b1/IGVFFI3652DBNT.fastq.gz",
    "schema_version": "14",
    "seqspecs": [
        "/configuration-files/IGVFFI2494UMAV/"
    ],
    "sequencing_kit": "NovaSeq 6000 S4 Reagent Kit v1.5",
    "sequencing_platform": {
        "@id": "/platform-terms/EFO_0008637/",
        "term_name": "Illumina NovaSeq 6000"
    },
    "sequencing_run": 3,
    "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/gRNA_CRISPRa_D3_S12_L003_R2_001.fastq.gz",
    "summary": "R2 reads from sequencing run 3",
    "upload_status": "validated",
    "uuid": "92f93e1d-90e7-403a-9b49-730fab6237b1"
}