IGVFDS5106XTZH

released
{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS5106XTZH/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5106XTZH",
    "aliases": [
        "charles-gersbach:cd8-tcells-analysis-set-crispr-ko-tfome"
    ],
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "audit": {
        "WARNING": [
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM2624KTRK](/primary-cells/IGVFSM2624KTRK/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_biosample_age",
                "path": "/primary-cells/IGVFSM2624KTRK/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM4936HKEW](/primary-cells/IGVFSM4936HKEW/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_biosample_age",
                "path": "/primary-cells/IGVFSM4936HKEW/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM0466RHGQ](/primary-cells/IGVFSM0466RHGQ/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_biosample_age",
                "path": "/primary-cells/IGVFSM0466RHGQ/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM7226CVDS](/primary-cells/IGVFSM7226CVDS/) is missing `upper_bound_age`, `lower_bound_age`, and `age_units`. Tissues, primary cells, and whole organisms are expected to specify a lower bound age, upper bound age, and age units.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_biosample_age",
                "path": "/primary-cells/IGVFSM7226CVDS/"
            }
        ]
    },
    "award": {
        "@id": "/awards/HG012053/",
        "component": "functional characterization",
        "contact_pi": {
            "@id": "/users/5d329c0e-3ea9-49bf-9bb9-844a53a882c0/",
            "title": "Charles Gersbach"
        },
        "title": "High-Throughput Functional Annotation of Gene Regulatory Elements and Variants Critical to Complex Cellular Phenotypes"
    },
    "control_for": [],
    "creation_timestamp": "2024-08-28T21:06:19.744257+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO4646JDEN/",
            "accession": "IGVFDO4646JDEN",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-23"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO6692QWLN/",
            "accession": "IGVFDO6692QWLN",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-24"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
    "files": [
        {
            "@id": "/tabular-files/IGVFFI9930ZUUB/",
            "accession": "IGVFFI9930ZUUB",
            "aliases": [
                "charles-gersbach:cd8-tcells-guide-counts-crispr-ko-tfome"
            ],
            "assembly": "custom",
            "content_type": "guide quantifications",
            "controlled_access": false,
            "creation_timestamp": "2024-09-20T18:39:36.212145+00:00",
            "file_format": "csv",
            "file_size": 146689,
            "href": "/tabular-files/IGVFFI9930ZUUB/@@download/IGVFFI9930ZUUB.csv.gz",
            "s3_uri": "s3://igvf-files/2024/09/20/3d775eae-5d57-47a2-bb4c-f58876ed6e2a/IGVFFI9930ZUUB.tsv.gz",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPR.TFome.ko.without.BATF3.counts.table.csv.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI8007AEGC/",
            "accession": "IGVFFI8007AEGC",
            "aliases": [
                "charles-gersbach:cd8-tcells-guide-quantifications-crispr-ko-tfome"
            ],
            "assembly": "custom",
            "content_type": "fold change over control",
            "controlled_access": false,
            "creation_timestamp": "2024-09-05T20:41:34.067052+00:00",
            "file_format": "tsv",
            "file_size": 364239,
            "href": "/tabular-files/IGVFFI8007AEGC/@@download/IGVFFI8007AEGC.tsv.gz",
            "s3_uri": "s3://igvf-files/2024/09/05/4a2e7a92-4227-4152-8f80-582df772a2a2/IGVFFI8007AEGC.tsv.gz",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T6A_DESeq2_TFko_screen_wo_BATF3.simple.v2.txt.gz",
            "upload_status": "validated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/analysis-sets/IGVFDS5551EATG/",
            "accession": "IGVFDS5551EATG",
            "aliases": [
                "charles-gersbach:cd8-tcells-intermediate-analysis-crispr-ko-tfome"
            ],
            "file_set_type": "intermediate analysis",
            "status": "released"
        }
    ],
    "input_for": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "protocols": [],
    "publications": [
        {
            "@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
            "publication_identifiers": [
                "PMID:37945901",
                "doi:10.1038/s41588-023-01554-0",
                "PMCID:PMC10703699"
            ],
            "status": "released"
        }
    ],
    "release_timestamp": "2024-11-18T21:09:10.759708+00:00",
    "sample_summary": "CD8-positive, alpha-beta memory T cell primary cell, modified with CRISPR modifications, transfected with a guide library, sorted on expression of IL7R",
    "samples": [
        {
            "@id": "/primary-cells/IGVFSM2624KTRK/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2624KTRK",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-low-bin-rep2"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS3667PLQB/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
                    "modality": "knockout",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/CL_0000909/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "CD8-positive, alpha-beta memory T cell",
                    "term_name": "CD8-positive, alpha-beta memory T cell"
                }
            ],
            "status": "released",
            "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/IGVFSM7226CVDS/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7226CVDS",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-high-bin-rep2"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS3667PLQB/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
                    "modality": "knockout",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/CL_0000909/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "CD8-positive, alpha-beta memory T cell",
                    "term_name": "CD8-positive, alpha-beta memory T cell"
                }
            ],
            "status": "released",
            "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/IGVFSM4936HKEW/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4936HKEW",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-low-bin-rep1"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS3667PLQB/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
                    "modality": "knockout",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/CL_0000909/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "CD8-positive, alpha-beta memory T cell",
                    "term_name": "CD8-positive, alpha-beta memory T cell"
                }
            ],
            "status": "released",
            "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/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM0466RHGQ",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-high-bin-rep1"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS3667PLQB/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/9fef21f2-9727-4a97-a5a7-c590a637c101/",
                    "modality": "knockout",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/CL_0000909/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "status": "released",
                    "summary": "CD8-positive, alpha-beta memory T cell",
                    "term_name": "CD8-positive, alpha-beta memory T cell"
                }
            ],
            "status": "released",
            "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"
        }
    ],
    "schema_version": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2024-09-05T20:41:34.067052+00:00",
    "summary": "CRISPR knockout FACS screen targeting IL7R: fold change over control, guide quantifications",
    "uuid": "72acda8d-d611-46e5-a41a-777570e148aa",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF8837BHJV/",
            "accession": "IGVFWF8837BHJV",
            "name": "Gersbach FACS CRISPR screen workflow",
            "status": "released"
        }
    ]
}