IGVFDS3461ZPPS

released
{
    "@context": "/terms/",
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    "@type": [
        "AnalysisSet",
        "FileSet",
        "Item"
    ],
    "accession": "IGVFDS3461ZPPS",
    "aliases": [
        "charles-gersbach:analysis-set-bulk-rna-DEanalysis"
    ],
    "assay_titles": [
        "RNA-seq"
    ],
    "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": "2024-10-25T22:48:02.114763+00:00",
    "donors": [
        {
            "@id": "/human-donors/IGVFDO3212TBUN/",
            "accession": "IGVFDO3212TBUN",
            "aliases": [
                "charles-gersbach:human-donor-WTC11"
            ],
            "sex": "male",
            "status": "released",
            "taxa": "Homo sapiens"
        }
    ],
    "file_set_type": "principal analysis",
    "files": [
        {
            "@id": "/tabular-files/IGVFFI9384YMLX/",
            "accession": "IGVFFI9384YMLX",
            "aliases": [
                "charles-gersbach:tabular-file-bulk-rna-count"
            ],
            "assembly": "GRCh38",
            "content_type": "transcript quantifications",
            "controlled_access": false,
            "creation_timestamp": "2024-10-24T17:16:51.749977+00:00",
            "file_format": "tsv",
            "file_size": 565376,
            "href": "/tabular-files/IGVFFI9384YMLX/@@download/IGVFFI9384YMLX.tsv.gz",
            "s3_uri": "s3://igvf-files/2024/10/24/c36d0f0f-7d1d-42ac-9d59-c1b0a39d3c7e/IGVFFI9384YMLX.tsv.gz",
            "status": "released",
            "submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/RNA/rnaseq_counts.tsv.gz",
            "upload_status": "validated"
        },
        {
            "@id": "/tabular-files/IGVFFI4480KZFW/",
            "accession": "IGVFFI4480KZFW",
            "aliases": [
                "charles-gersbach:tabular-file-bulk-rna-DEanalysis"
            ],
            "assembly": "GRCh38",
            "content_type": "fold change over control",
            "controlled_access": false,
            "creation_timestamp": "2024-10-28T13:51:17.373222+00:00",
            "file_format": "csv",
            "file_size": 780291,
            "href": "/tabular-files/IGVFFI4480KZFW/@@download/IGVFFI4480KZFW.csv.gz",
            "s3_uri": "s3://igvf-files/2024/10/28/9e7a4c9c-e78a-4302-af67-c4a177edd021/IGVFFI4480KZFW.csv.gz",
            "status": "released",
            "submitted_file_name": "/hpc/group/gersbachlab/tda17/IGVF_data_files/RNA/corrected_rnaseq_DE_analysis.csv.gz",
            "upload_status": "validated"
        }
    ],
    "functional_assay_mechanisms": [],
    "input_file_sets": [
        {
            "@id": "/analysis-sets/IGVFDS7046PDMA/",
            "accession": "IGVFDS7046PDMA",
            "aliases": [
                "charles-gersbach:analysis-set-bulk-rna-count"
            ],
            "file_set_type": "intermediate analysis",
            "status": "released"
        }
    ],
    "input_for": [],
    "lab": {
        "@id": "/labs/charles-gersbach/",
        "title": "Charles Gersbach, Duke"
    },
    "protocols": [],
    "release_timestamp": "2024-12-10T00:24:33.911927+00:00",
    "sample_summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell, at 1 time point(s) post change, antagonized with treatment(s)",
    "samples": [
        {
            "@id": "/in-vitro-systems/IGVFSM9734OHZN/",
            "@type": [
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                "Biosample",
                "Sample",
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            ],
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            ],
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            ],
            "sample_terms": [
                {
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                    ],
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                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens",
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                    "status": "released",
                    "treatment_term_name": "GSK3 inhibition"
                }
            ]
        },
        {
            "@id": "/in-vitro-systems/IGVFSM9140ULKM/",
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                "Biosample",
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                "Item"
            ],
            "accession": "IGVFSM9140ULKM",
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            ],
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                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
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            "@id": "/in-vitro-systems/IGVFSM7851SPEI/",
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            ],
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            ],
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                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM6721GJUT/",
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            ],
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            "aliases": [
                "charles-gersbach:in-vitro-system-bulk-rna-control-ipsc-cm-rep3"
            ],
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                "differentiated cell specimen"
            ],
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                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM7542AMUP/",
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                "Biosample",
                "Sample",
                "Item"
            ],
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            "aliases": [
                "charles-gersbach:in-vitro-system-bulk-rna-control-ipsc-cm-rep2"
            ],
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                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens"
        },
        {
            "@id": "/in-vitro-systems/IGVFSM2298AOEQ/",
            "@type": [
                "InVitroSystem",
                "Biosample",
                "Sample",
                "Item"
            ],
            "accession": "IGVFSM2298AOEQ",
            "aliases": [
                "charles-gersbach:in-vitro-system-bulk-rna-chir4um-ipsc-cm-rep3"
            ],
            "classifications": [
                "differentiated cell specimen"
            ],
            "sample_terms": [
                {
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                    "@type": [
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                        "OntologyTerm",
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                    ],
                    "aliases": [
                        "igvf:WTC11"
                    ],
                    "status": "released",
                    "summary": "GM25256 (WTC-11)",
                    "term_name": "GM25256 (WTC-11)"
                }
            ],
            "status": "released",
            "summary": "GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell for 28 days, male, Homo sapiens treated with 4 μM GSK3 inhibition for 7 days",
            "targeted_sample_term": {
                "@id": "/sample-terms/CL_0000746/",
                "status": "released",
                "term_name": "cardiac muscle cell"
            },
            "taxa": "Homo sapiens",
            "treatments": [
                {
                    "@id": "/treatments/98ba0c5c-8005-41bc-bcbb-6c6eff41af4e/",
                    "status": "released",
                    "treatment_term_name": "GSK3 inhibition"
                }
            ]
        }
    ],
    "schema_version": "9",
    "status": "released",
    "submitted_by": {
        "@id": "/users/3782ce69-0e9f-4b46-91f9-4578139785c7/",
        "title": "Ruhi Rai"
    },
    "submitted_files_timestamp": "2024-10-24T17:16:51.749977+00:00",
    "summary": "RNA-seq: fold change over control, transcript quantifications",
    "uuid": "d4ff7830-a109-489d-9522-1a20cf97281f",
    "workflows": [
        {
            "@id": "/workflows/IGVFWF6270QWBB/",
            "accession": "IGVFWF6270QWBB",
            "name": "Gersbach GGR RNA-seq Pipeline",
            "status": "released"
        }
    ]
}