Figure 6.

RNA-seq of irradiated and Smed-H2B(RNAi) samples. (a,b) Scatter plots of log10(RPKM) obtained for every transcript in irradiated day 2 versus non-irradiated samples (a) and Smed-H2B(RNAi) day 5 versus control(RNAi) samples (b). Category 1 (cat 1) genes described by Eisenhoffer and co-workers [24] are displayed in red, transcripts downregulated by irradiation described by Rossi and co-workers [25] in the planarian species Dugesia japonica are displayed in blue, and well known NB markers compiled from the literature are displayed in green. The scatter plot of irradiated versus non-irradiated samples is broader than that of Smed-H2B(RNAi) samples versus control(RNAi), indicating more drastic differences in relative gene expression. However, most colored transcripts lay below the diagonal, indicating their downregulation in both NB ablation approaches. (c) Density plot of percentage of relative expression compared to non-irradiated samples of irradiated samples 2, 4 and 7 days after irradiation (colored lines), and control(RNAi) samples (grey line). The differences in relative gene expression between irradiated samples and non-irradiated are very broad, with many transcripts being downregulated to 0 to 10% of their relative expression in non-irradiated samples. (d) Density plot of percentage of relative expression compared to control(RNAi) samples of Smed-H2B(RNAi) samples 1, 2 and 5 days after RNAi (colored lines), and non-irradiated samples (grey line). The differences in relative gene expression between Smed-H2B(RNAi) samples and control(RNAi) samples are narrower, with the majority of transcripts still presenting around 100% of their relative expression in non-irradiated samples.

Solana et al. Genome Biology 2012 13:R19   doi:10.1186/gb-2012-13-3-r19
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