IGVFDS0128XYUT

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS0128XYUT/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS0128XYUT",
    "aliases": [
        "charles-gersbach:jurkats-auxiliary-set-crispra-vp64-il2ra-high-bin-rep3"
    ],
    "audit": {
        "NOT_COMPLIANT": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS0128XYUT](/auxiliary-sets/IGVFDS0128XYUT/) has sequence file(s): [IGVFFI3109KTCA](/sequence-files/IGVFFI3109KTCA/) 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/IGVFDS0128XYUT/"
            }
        ]
    },
    "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": "2024-02-05T22:40:31.242681+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1648DRBT/",
            "accession": "IGVFDO1648DRBT",
            "aliases": [
                "charles-gersbach:jurkat-tcells-donor-3"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI3109KTCA/",
            "accession": "IGVFFI3109KTCA",
            "aliases": [
                "charles-gersbach:jurkats-measurement-set-crispra-vp64-il2ra-high-bin-rep3-R1"
            ],
            "content_type": "reads",
            "creation_timestamp": "2023-11-08T20:35:17.357399+00:00",
            "file_format": "fastq",
            "file_size": 26270837,
            "href": "/sequence-files/IGVFFI3109KTCA/@@download/IGVFFI3109KTCA.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/11/08/f26b75c8-51ca-4133-89f6-d078156d8b76/IGVFFI3109KTCA.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/pSM44-High-R3_S12_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5478QWPN/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS4959TRIO/",
            "accession": "IGVFDS4959TRIO",
            "aliases": [
                "charles-gersbach:jurkats-measurement-set-crispra-vp64-il2ra-high-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": "2024-11-18T21:08:55.134895+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM7748IVLZ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM7748IVLZ",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64-il2ra-high-bin-rep3"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "modality": "activation"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002796/",
                    "@type": [
                        "SampleTerm",
                        "OntologyTerm",
                        "Item"
                    ],
                    "aliases": [
                        "igvf:Jurkat"
                    ],
                    "status": "released",
                    "summary": "Jurkat",
                    "term_name": "Jurkat"
                }
            ],
            "status": "released",
            "summary": "Jurkat cell line, Homo sapiens (sorting details: FACS bin for 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-VP64, 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": "2023-11-08T20:35:17.357399+00:00",
    "summary": "gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in IL2RA",
    "uuid": "11a475d6-29f4-4cb3-a1d9-8d1b4c40803c"
}