Fig. 2

Temperature dependence of transcriptome in S2R+ and HB10 cells and adult male flies. (A, B) Aliquots of S2R+ cells and adult males were shifted to the indicated temperatures (11, 14, 25 and 30 °C) before RNA isolation (n = 3). A first experiment with S2R+ cells was analyzed with DNA microarrays, a second with S2R+ cells and adult males using 3′ RNA-Seq. (A) Pearson’s correlation coefficients after pairwise comparisons revealed maximal similarities between replicates from the same temperature and greater similarity of the transcriptomes at the lower temperatures (11 and 14 °C) compared to the higher temperatures (25 and 30 °C). (B) The number of CoolUp genes (blue dots) and CoolDown genes (red dots) with significantly different expression at the lower compared to the higher temperatures (FDR < 0.01; fold change ≥2). (C, D) Limited similarity of the transcriptome response to temperature change in S2R + cells and adult male flies. (C) Scatter plots of the fold changes of transcript levels (lower versus higher temperatures) either observed in the two experiments with S2R+ cells (top) or in the two 3′ RNA-Seq experiments with S2R+ cells and adult male flies (bottom). r = Pearson’s correlation coefficient. (D) Overlap among the top 300 CoolUp (left side) and CoolDown (right side) genes either in the two experiments with S2R+ cells (top) or in the two 3′ RNA-Seq experiments with S2R+ cells and adult male flies (bottom). (E) Transcriptome changes in response to low temperature in HB10 cells. Culture aliquots were shifted to the indicated temperatures (14 and 24 °C) before expression profiling. Pearson’s correlation coefficients obtained after pairwise comparison of the different samples, a volcano plot and a scatter plot are displayed