The Cell Cycle Regulated Transcriptome of Trypanosoma brucei
Figure 2
Expression profiling by DCE and RNA-seq.
A: Flow cytometry profiles of procyclic cells throughout the DCE selection procedure. Propidium iodide fluorescence (indicating DNA content) is measured on the x-axes and cell count on the y-axes. B: Regulation amplitude (the difference between the maximum and minimum expression value throughout the cell cycle) was calculated for each gene. After ranking genes according to minimum read count, the median (black) and upper and lower quartile (blue) amplitude values across a moving window of 100 genes was calculated. Genes with fewer than ∼300 reads in any time point (red line) gave amplitudes that were most likely to be a function of sequencing effort and were therefore excluded from further analysis. C: Comparison of gene regulatory amplitude between the starve-synch/microarray-analyzed cells (time points 5, 7 and 9 hrs) and DCE-synch/RNA seq-analyzed cells (time points 3, 5.5 and 7.25 hrs). Genes passing quality control in the RNA-seq experiment and with less than 1.23-fold regulation (0.3 log2 units - red lines) in both experiments (red box) were selected as a non-regulated control group for subsequent UTR sequence analyses (motif searching). D: Comparison of read counts per transcript for each time-point with the average read counts from the other 3 time points. Red boxes contain transcripts with >300 reads.