IGVFDS5741RXXI

{
    "@context": "/terms/",
    "@id": "/auxiliary-sets/IGVFDS5741RXXI/",
    "@type": [
        "AuxiliarySet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS5741RXXI",
    "aliases": [
        "charles-gersbach:jurkats-auxiliary-set-crispra-vp64x2-il2ra-low-bin-rep2"
    ],
    "audit": {
        "INTERNAL_ACTION": [
            {
                "category": "missing sequence specification",
                "detail": "Auxiliary set [IGVFDS5741RXXI](/auxiliary-sets/IGVFDS5741RXXI/) has sequence file(s): [IGVFFI4771IYRM](/sequence-files/IGVFFI4771IYRM/) 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/IGVFDS5741RXXI/"
            }
        ]
    },
    "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": "2024-02-05T22:40:25.962375+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO2560LMUL/",
            "accession": "IGVFDO2560LMUL",
            "aliases": [
                "charles-gersbach:jurkat-tcells-donor-5"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "gRNA sequencing",
    "files": [
        {
            "@id": "/sequence-files/IGVFFI4771IYRM/",
            "accession": "IGVFFI4771IYRM",
            "aliases": [
                "charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-low-bin-rep2-R1"
            ],
            "content_type": "reads",
            "controlled_access": false,
            "creation_timestamp": "2023-11-08T20:34:41.812727+00:00",
            "file_format": "fastq",
            "file_size": 21796194,
            "href": "/sequence-files/IGVFFI4771IYRM/@@download/IGVFFI4771IYRM.fastq.gz",
            "s3_uri": "s3://igvf-files/2023/11/08/6759a07d-6c0c-4a21-a08c-68542f12e201/IGVFFI4771IYRM.fastq.gz",
            "sequencing_platform": "/platform-terms/EFO_0004205/",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/raw_data/AIM_2_T_cell_project_1/pSM26-Low-R2_S3_L001_R1_001.fastq.gz",
            "upload_status": "validated"
        }
    ],
    "input_for": [
        "/analysis-sets/IGVFDS5218AVPW/"
    ],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "measurement_sets": [
        {
            "@id": "/measurement-sets/IGVFDS5042DREX/",
            "accession": "IGVFDS5042DREX",
            "aliases": [
                "charles-gersbach:jurkats-measurement-set-crispra-vp64x2-il2ra-low-bin-rep2"
            ],
            "preferred_assay_title": "CRISPR FACS screen",
            "status": "released"
        }
    ],
    "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": "2024-11-18T21:08:59.748115+00:00",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM2429HKWG/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2429HKWG",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64x2-il2ra-low-bin-rep2"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/4c532ce1-11aa-41be-9757-13923c19248b/",
                    "modality": "activation",
                    "status": "released"
                }
            ],
            "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 0-10% expression of IL2RA ) modified with CRISPRa Sa-dCas9-2xVP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        }
    ],
    "schema_version": "12",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2023-11-08T20:34:41.812727+00:00",
    "summary": "gRNA sequencing for CRISPR activation FACS screen integrating a guide (sgRNA) library targeting transcription start sites in IL2RA",
    "uuid": "db0d03f9-8456-4cb6-8d5a-30828c76e344"
}