IGVFFI4092OXMN

released
validated
{
    "@context": "/terms/",
    "@id": "/alignment-files/IGVFFI4092OXMN/",
    "@type": [
        "AlignmentFile",
        "File",
        "Item"
    ],
    "accession": "IGVFFI4092OXMN",
    "aliases": [
        "charles-gersbach:cd8-tcells-alignment-crispr-ko-tfome-low-bin-rep2"
    ],
    "analysis_step_version": "/analysis-step-versions/f9f6ae88-d515-4e49-9902-deea3cf87703/",
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "assembly": "custom",
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "mismatched status",
                "detail": "Released alignment file [IGVFFI4092OXMN](/alignment-files/IGVFFI4092OXMN/) has in progress subobject reference file [IGVFFI0626PVXM](/reference-files/IGVFFI0626PVXM/).",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_item_status",
                "path": "/alignment-files/IGVFFI4092OXMN/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization"
    },
    "content_md5sum": "7366c601f2b699680c166ebe226b2516",
    "content_summary": "unfiltered alignments",
    "content_type": "alignments",
    "controlled_access": false,
    "creation_timestamp": "2024-10-15T18:55:31.970109+00:00",
    "derived_from": [
        "/sequence-files/IGVFFI8518KWMY/"
    ],
    "file_format": "bam",
    "file_set": {
        "@id": "/analysis-sets/IGVFDS5551EATG/",
        "accession": "IGVFDS5551EATG",
        "file_set_type": "intermediate analysis",
        "samples": [
            {
                "@id": "/primary-cells/IGVFSM2624KTRK/",
                "accession": "IGVFSM2624KTRK",
                "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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM4936HKEW/",
                "accession": "IGVFSM4936HKEW",
                "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) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM0466RHGQ/",
                "accession": "IGVFSM0466RHGQ",
                "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 90-100% expression of IL7R) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            },
            {
                "@id": "/primary-cells/IGVFSM7226CVDS/",
                "accession": "IGVFSM7226CVDS",
                "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 90-100% expression of IL7R) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
                "taxa": "Homo sapiens"
            }
        ],
        "summary": "CRISPR knockout FACS screen targeting IL7R: alignments"
    },
    "file_size": 476837087,
    "filtered": false,
    "gene_list_for": [],
    "href": "/alignment-files/IGVFFI4092OXMN/@@download/IGVFFI4092OXMN.bam",
    "input_file_for": [
        "/tabular-files/IGVFFI9930ZUUB/"
    ],
    "integrated_in": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "loci_list_for": [],
    "md5sum": "d5870ccdcb3988e1a6c766b9e8453f84",
    "read_count": 39508748,
    "redacted": false,
    "reference_files": [
        "/reference-files/IGVFFI0626PVXM/"
    ],
    "release_timestamp": "2024-11-18T21:09:11.272385+00:00",
    "s3_uri": "s3://igvf-files/2024/10/15/8bb48d73-3903-4214-9146-8e99ec1c3a6f/IGVFFI4092OXMN.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/pSM73_L3_S3.sorted.bam",
    "summary": "custom assembly unfiltered alignments",
    "upload_status": "validated",
    "uuid": "8bb48d73-3903-4214-9146-8e99ec1c3a6f"
}