Additional file 4: Table S3. of Transcriptomes of newly-isolated Trypanosoma brucei rhodesiense reveal hundreds of mRNAs that are co-regulated with stumpy-form markers
Raw poly(A)+ mRNA transcriptome data and calculations based on reads per million (RPM). Sheet 1: Alignment statistics and correlations between the different datasets, calculated from RPM using the unique gene set only. cBS: cultured Lister 427 bloodstream forms expressing the tet repressor from pHD1313. BT1-3: Tbr729; LW - new isolates; PC - cultured Lister 427 procyclic forms. Sheet 2: Read counts for all genes. Sheet 3: Data for unique gene list [39] with reads per million (RPM). Column R shows the regulation pattern according to a custom script. Samples giving significantly peak RPMs (relative to other samples) are indicated by “max” and troughs are indicated by “min”. The threshold was set at 2-fold. Sheet 4: Sheet 3 results, filtered to remove genes for which the maximum RPM value was less than 10. Column T shows correlation coefficients of the RPM results with PIP39 (Tb927.9.6090). Colour code for ratios: Blue is less than 0.25×, green is less than 0.5×, orange is greater than 2× and red is greater than 4×. Comparisons with other datasets 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. Sheet 5: calculated RPMs for selected recognised stumpy-form markers. Reads for the ESAG9s and the PAD genes are not unique and precise allocation to a particular variant was not attempted. Sheet 6: Genes showing increased RPM values in both LW032 and LW042 and metacyclic (salivary gland, SG) forms. Sheet 7: Genes showing reduced RPM values in both LW032 and LW042 and metacyclic (salivary gland, SG) forms. (XLSX 3928 kb
