IGVFDS5417LSWU

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS5417LSWU/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5417LSWU",
    "aliases": [
        "charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-high-bin-rep3"
    ],
    "assay_term": {
        "@id": "/assay-terms/OBI_0003661/",
        "status": "released",
        "term_name": "in vitro CRISPR screen using flow cytometry"
    },
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS9310VIMF](/auxiliary-sets/IGVFDS9310VIMF/) has sequence file(s): [IGVFFI7647ERJF](/sequence-files/IGVFFI7647ERJF/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 30,
                "level_name": "INTERNAL_ACTION",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS9310VIMF/"
            }
        ],
        "WARNING": [
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM1721KPGX](/primary-cells/IGVFSM1721KPGX/) 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/IGVFSM1721KPGX/"
            },
            {
                "category": "missing files",
                "detail": "Measurement set [IGVFDS5417LSWU](/measurement-sets/IGVFDS5417LSWU/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/measurement-sets/IGVFDS5417LSWU/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS5417LSWU](/measurement-sets/IGVFDS5417LSWU/) has no cell sorting `auxiliary_sets`. CRISPR-based measurement sets that utilize flow cytometry are expected to link to a cell sorting auxiliary set.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_missing_auxiliary_set",
                "path": "/measurement-sets/IGVFDS5417LSWU/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS9310VIMF/",
            "accession": "IGVFDS9310VIMF",
            "aliases": [
                "charles-gersbach:cd8-tcells-auxiliary-set-crispra-ccr7-high-bin-rep3"
            ],
            "file_set_type": "gRNA sequencing",
            "status": "released"
        }
    ],
    "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_file_sets": [
        {
            "@id": "/measurement-sets/IGVFDS6262JHMS/",
            "accession": "IGVFDS6262JHMS",
            "aliases": [
                "charles-gersbach:cd8-tcells-measurement-set-crispra-ccr7-low-bin-rep3"
            ],
            "status": "released"
        }
    ],
    "control_for": [],
    "creation_timestamp": "2023-11-08T19:32:54.207305+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO4579FYIL/",
            "accession": "IGVFDO4579FYIL",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-22"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "externally_hosted": false,
    "file_set_type": "experimental data",
    "files": [],
    "input_for": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "notes": "The readout 2e41e624-f6c7-4f0c-a07e-bc36cefdca39 was removed from this measurement set. This file_set previously had 5d15ca93-89fb-4a34-8863-001eda25bb4c submitted as library_construction_platform, but the property library_construction_platform has been now removed.",
    "preferred_assay_title": "CRISPR FACS screen",
    "protocols": [
        "https://www.protocols.io/view/car-t-cell-characterization-by-flow-cytometry-c48qyzvw",
        "https://www.protocols.io/view/crispra-tiling-screens-c5rfy53n"
    ],
    "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": "2024-11-19T20:34:42.031253+00:00",
    "samples": [
        {
            "@id": "/primary-cells/IGVFSM1721KPGX/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1721KPGX",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispra-ccr7-high-bin-rep3"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS4163YHBI/",
                    "accession": "IGVFDS4163YHBI",
                    "file_set_type": "guide library",
                    "status": "released",
                    "summary": "guide (sgRNA) library targeting transcription start sites in many genes"
                }
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "modality": "activation",
                    "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 CCR7) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "23",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2023-11-08T20:33:58.631828+00:00",
    "summary": "CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000126353/",
            "geneid": "ENSG00000126353",
            "name": "C-C motif chemokine receptor 7",
            "status": "released",
            "symbol": "CCR7",
            "synonyms": [
                "lymphocyte-specific G protein-coupled peptide receptor",
                "Bukitt's lymphoma receptor 2",
                "EBV-induced G protein-coupled receptor 1",
                "EBI1",
                "BLR2",
                "chemokine (C-C motif) receptor 7",
                "CMKBR7",
                "CDw197",
                "Epstein-Barr virus induced gene 1",
                "MIP-3 beta receptor",
                "CD197",
                "Epstein-Barr virus-induced G-protein coupled receptor 1",
                "C-C chemokine receptor type 7",
                "CCR-7",
                "CC chemokine receptor 7",
                "CC-CKR-7"
            ]
        }
    ],
    "uuid": "de560adb-339a-415c-aec8-7b938364bbfd"
}