Transcriptomic profiling of splenic B lymphomas spontaneously developed in B cell-specific TRAF3-deficient mice.

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Specific deletion of TRAF3 from B lymphocytes leads to spontaneous development of marginal zone lymphomas (MZL) or B1 lymphomas in mice. To identify novel oncogenes and tumor suppressive genes involved in malignant transformation of TRAF3-deficient B cells, we performed a microarray analysis to identify genes differentially expressed in TRAF3-/- mouse splenic B lymphomas. We have identified 160 up-regulated genes and 244 down-regulated genes in TRAF3-/- B lymphomas as compared to littermate control splenocytes. Here we describe the samples, quality control assessment, as well as the data analysis methods in detail for the transcriptomic profiling study. 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[8]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using limma modeling with empirical Bayes moderation, the study identified 160 up-regulated and 244 down-regulated genes in TRAF3−/− B lymphomas; the source data are archived at NIH GEO under accession GSE48818.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:25419513", "locator": "sections[7] \"Statistics\" paragraph 2", "quote": "Statistical analyses were performed using limma modeling (ANOVA with empirical Bayes moderation of standard errors)."}, {"asset": "source:pmid:25419513", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We have identified 160 up-regulated genes and 244 down-regulated genes in TRAF3−/−B lymphomas as compared to littermate control splenocytes."}, {"asset": "source:pmid:25419513", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data are archived at NIH GEO with accession number GSE48818."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using limma modeling with empirical Bayes moderation, the study identified 160 up-regulated and 244 down-regulated genes in TRAF3−/− B lymphomas; the source data are archived at NIH GEO under accession GSE48818.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:25419513"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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To identify novel oncogenes and tumor suppr", "y genes differentially expressed in TRAF3-/- mouse splenic B lymphomas. We have identified 160", "elected TRAF3−/− splenic B lymphoma samples (mouse ID: 6983-2, 7041-10, and 7060-8), B lymphoma", "s for all seven samples as identified by the Mouse ID (see Table 1). (B) Bioanalyzer output as"], "order_basis": "paper_text_order:313", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["n of TRAF3-deficient B cells, we performed a microarray analysis to identify genes differentially ex", ". RNA samples for transcriptome profiling by microarray analysis. Quality control assay of RNAs used", "≥ 1 (Fig. 2). Volcano plot of limma-modeled microarray data. The data for all genes are plotted as", ", which was chosen for further analysis [8]. Microarray data are available from NIH GEO Accession GS"], "order_basis": "paper_text_order:458", "id": "assay:2"}, {"role": "data_generation", "definition_id": "flow_cytometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ma cells are > 70% of B cells as assessed by FACS analysis of B cell populations and Southern"], "order_basis": "paper_text_order:1269", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical analyses were performed using limma modeling (ANOVA with empirical Bayes moderation of standard errors)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}