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Additional file 18: Table S4. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

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posted on 26.04.2016, 05:00 by Enoch Antwi, Jurgen Haanstra, Gowthaman Ramasamy, Bryan Jensen, Dorothea Droll, Federico Rojas, Igor Minia, Monica Terrao, Clémentine Mercé, Keith Matthews, Peter Myler, Marilyn Parsons, Christine Clayton
Ribosome profiling data. Jensen - data from [20]; Silicotryp - data from [16] and this paper. All numbers were suitably rounded after the calculations had been finished. Gene annotation is partly from tritrypDB and partly manual. Sheet 1: Raw read counts for all ORFs. RP = ribosome profiling, FR = fragmented poly(A) + RNA. BS = bloodstream, PC = procyclic. Sheet 2: Reads for the unique gene set of genes [9], used in subsequent calculations. Sheet 3: DeSeq comparison of Jensen and Silicotryp results (total ribosome profiling reads per ORF) for procyclic forms. Sheet 4: DeSeq comparison of Jensen and Silicotryp results (total ribosome profiling reads per ORF) for bloodstream forms. Sheet 5: DeSeq comparison of Jensen and Silicotryp results (total fragmented RNA reads per ORF) for procyclic forms. Sheet 6: DeSeq comparison of Jensen and Silicotryp results (total fragmented RNA reads per ORF) for bloodstream forms. Sheet 7: ORFs that showed significant differences in ribosome profiling reads between the Jensen and Silicotryp datasets. Red are higher in Silicotryp and blue are lower. Sheet 8: Reads per million calculated for the unique gene set. Sheet 9: Alignment statistics. rp = ribosome profiling; fr = fragmented poly(A) + RNA. PC- = procyclic, BS = cultured bloodstream forms. Sheet 10: Alternative normalisation using EdgeR. (XLSX 7622 kb)

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Deutsche Forschungsgemeinschaft

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