Figure 4

Scatter plots of transcriptome data from trypanosomes subjected to altered culturing conditions and other challenges. In each case, Cy5 fluorescence is plotted on the Y-axis and Cy3 fluorescence on the X-axis. Spots with a Cy5/Cy3 or Cy3/Cy5 ratio above two, i.e. significantly differentially expressed are highlighted in black, spots with a ratio below two are shown in grey. Panel A: BSF (Cy5) vs PCF (Cy3); data are identical to Figure 1 and reproduced for comparison. Panel B: BSF in 30% FBS (Cy5) vs BSF (Cy3). Panel C: BSF (Cy5) vs BSF in 0% FBS, 5 mg/ml BSA (Cy3). Panel D: BSF (Cy5) vs BSF in 0% FBS, 5 mg/ml, BSA 0.3 mg/ml Tfn (Cy3). Panel E: BSF in 1 mM DTT for 1 hr (Cy5) vs BSF (Cy3). Panel F: BSF in 1 mM DTT for 4 hr (Cy5) vs BSF (Cy3). Panel G: BSF in 5 μg/ml tunicamycin for 4 hr (Cy5) vs BSF (Cy3). Panel H: BSF in 5 μg/ml tunicamycin for 24 hr (Cy5) vs BSF (Cy3). Panel I: VSG RNAi in BSF, induced for 24 hr (Cy5) vs uninduced (Cy3). Panel J: VSG RNAi in BSF, induced for 72 hr (Cy5) vs uninduced (Cy3). Panel K: CLH RNAi in BSF, induced for 24 hr (Cy5) vs uninduced (Cy3). Panel L: BSF (Cy5) vs MITat1.1 grown in vivo in rats (Cy3). The scatter plots for most experiments (panels B-K) indicate few transcripts that fall outside of the region considered as constitutive, in marked contrast to the scattergrams obtained for developmental changes (panel A) and in the comparison between in vitro versus in vivo BSF cultures (panel L).