IGVFDS7413JPIS

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS7413JPIS/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS7413JPIS",
    "aliases": [
        "charles-gersbach:cd8-tcells-auxiliary-set-crispri-cd2-low-bin-rep3"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS7413JPIS](/auxiliary-sets/IGVFDS7413JPIS/) has sequence file(s): [IGVFFI2791EHZO](/sequence-files/IGVFFI2791EHZO/) which do not have any `seqspecs`. Sequence files in a file set are expected to link to a sequence specification file.",
                "level": 50,
                "level_name": "NOT_COMPLIANT",
                "name": "audit_missing_seqspec",
                "path": "/auxiliary-sets/IGVFDS7413JPIS/"
            }
        ],
        "WARNING": [
            {
                "category": "missing age",
                "detail": "Primary cell [IGVFSM6350DJQS](/primary-cells/IGVFSM6350DJQS/) 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/IGVFSM6350DJQS/"
            }
        ]
    },
    "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": "2024-02-05T22:39:15.732273+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1423VLXL/",
            "accession": "IGVFDO1423VLXL",
            "aliases": [
                "charles-gersbach:cd8-tcells-donor-16"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI2791EHZO/",
            "accession": "IGVFFI2791EHZO",
            "aliases": [
                "charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-low-bin-rep3-R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-11-08T20:27:22.715991+00:00",
            "file_format": "fastq",
            "file_size": 33730039,
            "href": "/sequence-files/IGVFFI2791EHZO/@@download/IGVFFI2791EHZO.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/11/08/e0614745-755c-4af2-81e6-b0d769d12371/IGVFFI2791EHZO.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0004205/",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM8-Low-R3_S16_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5498STRV/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4663XDBF/",
            "accession": "IGVFDS4663XDBF",
            "aliases": [
                "charles-gersbach:cd8-tcells-measurement-set-crispri-cd2-low-bin-rep3"
            ],
            "preferred_assay_title": "CRISPR FACS screen"
        }
    ],
    "publications": [
        {
            "@id": "/publications/6cc80a53-4ca1-4bd4-9942-f0f335b7ec20/",
            "publication_identifiers": [
                "PMID:37945901",
                "doi:10.1038/s41588-023-01554-0",
                "PMCID:PMC10703699"
            ]
        }
    ],
    "release_timestamp": "2024-11-18T21:09:03.772246+00:00",
    "samples": [
        {
            "@id": "/primary-cells/IGVFSM6350DJQS/",
            "@type": [
                "PrimaryCell",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM6350DJQS",
            "aliases": [
                "charles-gersbach:cd8-tcells-primary-cell-crispri-cd2-low-bin-rep3"
            ],
            "classifications": [
                "primary cell"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8345ZMZW/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/95393c9a-637d-43f6-baf9-662e45d28d61/",
                    "modality": "interference"
                }
            ],
            "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 CD2) modified with CRISPRi Sa-dCas9, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "11",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2023-11-08T20:27:22.715991+00:00",
    "summary": "gRNA sequencing for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in CD2",
    "uuid": "7c7c7c10-6fe6-44ef-a358-1fb32d942683"
}