Additional file 5: Table S4. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers

Transcriptome analysis using DESeq. Sheet 1: Using only the unique gene set, transcriptomes from different isolates were compared pair-wise using DESeq. We show only the fold change and the adjusted P-values. Background colours are used only to make the pairs clear. Sheet 2: mRNAs that are most specifically increased in the LW032 and LW042 trasncriptomes relative to cBS, BT, and PC. Only genes with with adjusted P-values of less than 0.01 were considered. Of these, at least one isolate (either 42 or 32) had to show a 3-fold increase relative to cultured bloodstream forms, and the remainder of the ratios had to be at least 2× cBS or BT. B42 or 32 also had to be at least 2-fold procyclics. Comparisons with other datasets in this and subsequent sheets are indicated as follows: ST/SL Kabani; stumpy/slender ratio from [6]; ST/SL BS Jensen -stumpy/slender ratio from [7]; SLvST mRNA Capewell and ST polysomes/mRNA Capewell - data from [13]; SG/cBS: salivary gland trypanosomes relative to cultured bloodstream forms from [30]; SG/PC: salivary gland trypanosomes [30] relative to our results for cultured Lister 427 procyclic forms: cell cycle peak and amplitude: data from [31]. RITSeq: data from [28]. Sheet 3: mRNAs increased in procyclics as well as in LW032 and LW042. As for sheet 2 except that results for B42 and B32 had to be more than 0.5× the procyclic value. Sheet 4: mRNAs decreased at least two-fold in LW032 and LW042 relative to procyclics and bloodstream forms. Calculations similar to sheet 2. Sheet 5: mRNAs that were at least 3-fold higher in cBS relative to the other conditions. Sheet 6: mRNAs that were low in all parasites isolated from blood (down in BT as well as the recent isolates). (XLSX 4058 kb)