IGVFFI7658XOUY

released
validated
{
    "@context": "/terms/",
    "@id": "/alignment-files/IGVFFI7658XOUY/",
    "@type": [
        "AlignmentFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI7658XOUY",
    "aliases": [
        "charles-gersbach:cd8-tcells-alignment-crispri-ccr7-high-bin-rep1"
    ],
    "analysis_step_version": "/analysis-step-versions/f9f6ae88-d515-4e49-9902-deea3cf87703/",
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "assembly": "custom",
    "audit": {},
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "6d610ede943c88fbc48f58a9988904ff",
    "content_summary": "unfiltered alignments",
    "content_type": "alignments",
    "controlled_access": false,
    "creation_timestamp": "2024-10-15T18:59:21.594747+00:00",
    "derived_from": [
        "/sequence-files/IGVFFI6405ADNH/"
    ],
    "file_format": "bam",
    "file_set": {
        "@id": "/analysis-sets/IGVFDS9065THHI/",
        "accession": "IGVFDS9065THHI",
        "file_set_type": "intermediate analysis",
        "samples": [
            {
                "@id": "/primary-cells/IGVFSM9398LTWW/",
                "accession": "IGVFSM9398LTWW",
                "classifications": [
                    "primary cell"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
                        "modality": "interference",
                        "summary": "CRISPRi Sa-dCas9"
                    }
                ],
                "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 CCR7) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM7413JCSK/",
                "accession": "IGVFSM7413JCSK",
                "classifications": [
                    "primary cell"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
                        "modality": "interference",
                        "summary": "CRISPRi Sa-dCas9"
                    }
                ],
                "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 CCR7) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM2207SJEN/",
                "accession": "IGVFSM2207SJEN",
                "classifications": [
                    "primary cell"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
                        "modality": "interference",
                        "summary": "CRISPRi Sa-dCas9"
                    }
                ],
                "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 CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM1205VMNO/",
                "accession": "IGVFSM1205VMNO",
                "classifications": [
                    "primary cell"
                ],
                "modifications": [
                    {
                        "@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
                        "modality": "interference",
                        "summary": "CRISPRi Sa-dCas9"
                    }
                ],
                "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 CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "CRISPR interference FACS screen targeting CCR7: alignments"
    },
    "file_size": 13972258,
    "filtered": false,
    "gene_list_for": [],
    "href": "/alignment-files/IGVFFI7658XOUY/@@download/IGVFFI7658XOUY.bam",
    "input_file_for": [
        "/tabular-files/IGVFFI3289WICA/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "loci_list_for": [],
    "md5sum": "2f41318579ffb1e29296058830833419",
    "read_count": 805013,
    "redacted": false,
    "reference_files": [
        "/reference-files/IGVFFI6999YLZG/"
    ],
    "release_timestamp": "2024-11-18T21:09:09.313176+00:00",
    "s3_uri": "s3://igvf-files/2024/10/15/7ecff3f4-5e98-4d37-8121-c79cffe3f0f9/IGVFFI7658XOUY.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/CCR7pos-pSM27-TF-H1_S2.sorted.bam",
    "summary": "custom assembly unfiltered alignments",
    "upload_status": "validated",
    "uuid": "7ecff3f4-5e98-4d37-8121-c79cffe3f0f9"
}