IGVFDS2261TIMI

released
{
    "@context": "/terms/",
    "@id": "/analysis-sets/IGVFDS2261TIMI/",
    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS2261TIMI",
    "aliases": [
        "charles-gersbach:jurkats-analysis-set-crispra-vp64-il2ra"
    ],
    "assay_titles": [
        "CRISPR FACS screen"
    ],
    "audit": {},
    "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": "2024-08-28T21:06:23.398146+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO1648DRBT/",
            "accession": "IGVFDO1648DRBT",
            "aliases": [
                "charles-gersbach:jurkat-tcells-donor-3"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO0512VHUM/",
            "accession": "IGVFDO0512VHUM",
            "aliases": [
                "charles-gersbach:jurkat-tcells-donor-1"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/human-donors/IGVFDO2154QIFS/",
            "accession": "IGVFDO2154QIFS",
            "aliases": [
                "charles-gersbach:jurkat-tcells-donor-2"
            ],
            "sex": "unspecified",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
    "files": [
        {
            "@id": "/tabular-files/IGVFFI7694LAUN/",
            "accession": "IGVFFI7694LAUN",
            "aliases": [
                "charles-gersbach:jurkats-guide-counts-crispra-vp64-il2ra"
            ],
            "assembly": "custom",
            "content_type": "guide quantifications",
            "controlled_access": false,
            "creation_timestamp": "2024-09-20T18:40:14.852795+00:00",
            "file_format": "csv",
            "file_size": 9375,
            "href": "/tabular-files/IGVFFI7694LAUN/@@download/IGVFFI7694LAUN.csv.gz",
            "s3_uri": "s3://igvf-files/2024/09/20/04b777a2-5036-408c-8914-76bb4464b853/IGVFFI7694LAUN.tsv.gz",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/CRISPRa.1xVP64.IL2RA.counts.table.csv.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI2207HLUJ/",
            "accession": "IGVFFI2207HLUJ",
            "aliases": [
                "charles-gersbach:jurkats-guide-quantifications-crispra-vp64-il2ra"
            ],
            "assembly": "custom",
            "content_type": "fold change over control",
            "controlled_access": false,
            "creation_timestamp": "2024-09-05T20:41:01.036658+00:00",
            "file_format": "tsv",
            "file_size": 13760,
            "href": "/tabular-files/IGVFFI2207HLUJ/@@download/IGVFFI2207HLUJ.tsv.gz",
            "s3_uri": "s3://igvf-files/2024/09/05/9df28753-7e21-410f-a84c-013b23eda694/IGVFFI2207HLUJ.tsv.gz",
            "status": "released",
            "submitted_file_name": "/data/reddylab/Alex/IGVF/data_submissions/processed_data/AIM_2_T_cell_project_1/T1C_IL2RA_CRISPRa1xVP64_screen.simple.v2.txt.gz",
            "upload_status": "validated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/analysis-sets/IGVFDS5478QWPN/",
            "accession": "IGVFDS5478QWPN",
            "aliases": [
                "charles-gersbach:jurkats-intermediate-analysis-crispra-vp64-il2ra"
            ],
            "file_set_type": "intermediate analysis",
            "status": "released"
        }
    ],
    "input_for": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "protocols": [],
    "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": "2024-11-18T21:09:17.860141+00:00",
    "sample_summary": "Jurkat cell line, modified with CRISPR modifications, transfected with a guide library, sorted on expression of IL2RA",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM3148FRBY/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3148FRBY",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64-il2ra-high-bin-rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "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 90-100% expression of IL2RA ) modified with CRISPRa Sa-dCas9-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM1480DJBL/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM1480DJBL",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64-il2ra-low-bin-rep1"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "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-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        },
        {
            "@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",
                    "status": "released"
                }
            ],
            "sample_terms": [
                {
                    "@id": "/sample-terms/EFO_0002796/",
                    "@type": [
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                        "OntologyTerm",
                        "Item"
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                    "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"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM3606VJWU/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM3606VJWU",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64-il2ra-low-bin-rep3"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "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-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM4401YRWQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM4401YRWQ",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64-il2ra-low-bin-rep2"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "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-VP64, transduced (lentivirus) with a guide library (MOI of 0.4)",
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM2737ATVK/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2737ATVK",
            "aliases": [
                "charles-gersbach:jurkats-in-vitro-system-crispra-vp64-il2ra-high-bin-rep2"
            ],
            "classifications": [
                "cell line"
            ],
            "construct_library_sets": [
                "/construct-library-sets/IGVFDS8183QSJO/"
            ],
            "modifications": [
                {
                    "@id": "/crispr-modifications/2c49eb31-f10b-47b7-b260-4f720014ad79/",
                    "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 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": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/29f5f78d-ac90-421e-90c6-a90e1dc407a7/",
        "title": "Alejandro Barrera"
    },
    "submitted_files_timestamp": "2024-09-05T20:41:01.036658+00:00",
    "summary": "CRISPR activation FACS screen targeting IL2RA: fold change over control, guide quantifications",
    "uuid": "4205ba9f-8b39-413f-ab5f-7f9c29d55b8d",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF8837BHJV/",
            "accession": "IGVFWF8837BHJV",
            "name": "Gersbach FACS CRISPR screen workflow",
            "status": "released"
        }
    ]
}