IGVFDS8967NSST

released
{
    "@context": "/terms/",
    "@id": "/measurement-sets/IGVFDS8967NSST/",
    "@type": [
        "MeasurementSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS8967NSST",
    "aliases": [
        "charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-low-bin-rep2"
    ],
    "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 [IGVFDS4170XDRQ](/auxiliary-sets/IGVFDS4170XDRQ/) has sequence file(s): [IGVFFI2908JEGF](/sequence-files/IGVFFI2908JEGF/) 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/IGVFDS4170XDRQ/"
            }
        ],
        "WARNING": [
            {
                "category": "missing files",
                "detail": "Measurement set [IGVFDS8967NSST](/measurement-sets/IGVFDS8967NSST/) has no `files`. File sets are expected to have files.",
                "level": 40,
                "level_name": "WARNING",
                "name": "audit_no_files",
                "path": "/measurement-sets/IGVFDS8967NSST/"
            },
            {
                "category": "missing auxiliary set",
                "detail": "Measurement set [IGVFDS8967NSST](/measurement-sets/IGVFDS8967NSST/) 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/IGVFDS8967NSST/"
            },
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM7158ADKU](/primary-cells/IGVFSM7158ADKU/) 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/IGVFSM7158ADKU/"
            }
        ]
    },
    "auxiliary_sets": [
        {
            "@id": "/auxiliary-sets/IGVFDS4170XDRQ/",
            "accession": "IGVFDS4170XDRQ",
            "aliases": [
                "charles-gersbach:cd8-tcells-auxiliary-set-crispr-ko-tfome-batf3-over-low-bin-rep2"
            ],
            "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_for": [
        {
            "@id": "/measurement-sets/IGVFDS4325LQED/",
            "accession": "IGVFDS4325LQED",
            "aliases": [
                "charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-high-bin-rep2"
            ],
            "status": "released"
        }
    ],
    "creation_timestamp": "2023-11-08T19:32:41.819307+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2763RVOY/",
            "accession": "IGVFDO2763RVOY",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-26"
            ],
            "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/tfome-crisprko-screens-81wgbxk8olpk/v1"
    ],
    "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": "2024-11-19T20:34:00.388920+00:00",
    "samples": [
        {
            "@id": "/primary-cells/IGVFSM7158ADKU/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7158ADKU",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispr-ko-tfome-batf3-over-low-bin-rep2"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                {
                    "@id": "/construct-library-sets/IGVFDS3667PLQB/",
                    "accession": "IGVFDS3667PLQB",
                    "file_set_type": "guide library",
                    "status": "released",
                    "summary": "guide (sgRNA) library targeting transcription start sites in many genes"
                }
            ],
            "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 in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, 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": "2023-11-08T20:30:23.967927+00:00",
    "summary": "CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes",
    "targeted_genes": [
        {
            "@id": "/genes/ENSG00000168685/",
            "geneid": "ENSG00000168685",
            "name": "interleukin 7 receptor",
            "status": "released",
            "symbol": "IL7R",
            "synonyms": [
                "CD127 antigen",
                "CDW127",
                "soluble interleukin-7 receptor",
                "IL7Ralpha",
                "IL-7R subunit alpha",
                "sIL-7R",
                "IL-7 receptor subunit alpha",
                "lnc-IL7R",
                "IL7RA",
                "IMD104",
                "CD127",
                "ILRA",
                "IL-7Ralpha",
                "interleukin-7 receptor subunit alpha",
                "interleukin 7 receptor alpha chain",
                "IL-7R-alpha"
            ]
        }
    ],
    "uuid": "ca4a46c8-0fe6-423a-b181-5c94732c02a6"
}