Additional file 19: Table S5. of Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

Ribosome density calculations and comparisons. Sheet 1. Ribosome densities in procyclic forms. The average number of ribosomes per ORF was calculated as follows. First, we needed to correct the ribosome profiling results for the gene copy number in the genome assembly, since during the initial alignments, the reads had been spread out among all orthologues. Orthologue counts were taken from TritrypDB. Unexpected numbers were checked against our previous read alignment data [20], and in some cases manually. Read results for some gene families (such as amino acid transporters) are unreliable because related genes show different regulation. The orthologue counts used are in column D. All RPM were multiplied by the orthologue count (column H). Numbers of mRNAs per cell [16] were previously calculated assuming a total of 19,000 non-VSG mRNAs in bloodstream forms, and 43,000 non-EP-procyclin mRNAs/cell in procyclics [17]. There are about 275000 ribosomes per procyclic parasite and 125000 per bloodstream form [17]. The ribosome densities are calculated using these numbers. In practice, the densities are likely to be lower. About 5 % of ribosomes are likely to be on ORFs that were excluded from the analysis (Procyclin, VSG, ESAGs, and from repetitive elements). Approximately 70 % of all ribosomal RNA is in polysomes, 20 % is in monosomes and the rest is in subunits (our unpublished results); we do not know what proportion of the ribosomes in the monosomal fraction is engaged in translation. Sheet 2. Ribosome densities in bloodstream forms. Sheet 3. Ribosome densities and half-lives in procyclic forms, using only the “reliable” values that were chosen for modelling. Sheet 4. Ribosome densities and half-lives in bloodstream forms, using only the “reliable” values that were chosen for modelling. (XLSX 2688 kb)