IGVFFI3628DFGJ

{
    "@context": "/terms/",
    "@id": "/alignment-files/IGVFFI3628DFGJ/",
    "@type": [
        "AlignmentFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI3628DFGJ",
    "aliases": [
        "charles-gersbach:cd8-tcells-rna-seq-cas-ko-znf217-bam-rep1"
    ],
    "analysis_step_version": "/analysis-step-versions/7298947c-9675-4de2-933a-642bde562751/",
    "assay_titles": [
        "RNA-seq"
    ],
    "assembly": "GRCh38",
    "audit": {},
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "bdbbde718a6964825c0583d35103fa2b",
    "content_summary": "filtered transcriptome alignments",
    "content_type": "transcriptome alignments",
    "controlled_access": false,
    "creation_timestamp": "2024-10-14T20:59:34.263824+00:00",
    "derived_from": [
        "/sequence-files/IGVFFI0020UHMA/",
        "/sequence-files/IGVFFI5010ENZG/"
    ],
    "file_format": "bam",
    "file_set": {
        "@id": "/analysis-sets/IGVFDS4430NOFL/",
        "accession": "IGVFDS4430NOFL",
        "file_set_type": "intermediate analysis",
        "samples": [
            {
                "@id": "/primary-cells/IGVFSM1311HWOF/",
                "accession": "IGVFSM1311HWOF",
                "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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM5949AWIH/",
                "accession": "IGVFSM5949AWIH",
                "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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM5367RVVU/",
                "accession": "IGVFSM5367RVVU",
                "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 modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "knockout RNA-seq: transcriptome alignments"
    },
    "file_size": 2159921921,
    "filtered": true,
    "gene_list_for": [],
    "href": "/alignment-files/IGVFFI3628DFGJ/@@download/IGVFFI3628DFGJ.bam",
    "input_file_for": [
        "/tabular-files/IGVFFI7900YIDY/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "loci_list_for": [],
    "md5sum": "5a0f2163072faa5d93ac04c84e5e37ef",
    "read_count": 49649123,
    "redacted": false,
    "reference_files": [
        "/reference-files/IGVFFI0653VCGH/"
    ],
    "release_timestamp": "2024-10-25T04:18:40.512348+00:00",
    "s3_uri": "s3://igvf-files/2024/10/14/2d7652c0-a791-43fd-b7d4-3462bd9e8457/IGVFFI3628DFGJ.bam",
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/cd8.rnaseq.pSM73.znf217.d1.star2.Aligned.out.sorted.bam",
    "summary": "GRCh38 filtered transcriptome alignments",
    "upload_status": "validated",
    "uuid": "2d7652c0-a791-43fd-b7d4-3462bd9e8457"
}