Extraction of transcripts confidently expressed in NBs by a combined irradiation and Smed-H2B RNAi approach. (a) Venn diagram of the number of transcripts downregulated in irradiated (green) and Smed-H2B(RNAi) (blue) samples. Irradiation downregulates more than half of our dataset of 17,262 transcripts. Smed-H2B(RNAi) downregulates less than 10% of the total number of transcripts. Most transcripts downregulated by Smed-H2B RNAi are also downregulated in irradiated samples (P ≈ 0). (b-e) Δ Fold changes (ΔFC) between consecutive time points of irradiated (b,d) and Smed-H2B(RNAi) (c,e) samples. Most transcripts in irradiated samples tend to accumulate at the axis of the plot, indicating that their relative expression values in the three time points are similar (b). Most transcripts in Smed-H2B(RNAi) samples tend to accumulate in the bottom left quadrant, indicating that their relative expression values tend to be progressively lower (c). After filtering of transcripts that have fold changes of more than 0.2 or -0.2 in consecutive irradiation samples and of more than 0.2 in consecutive Smed-H2B(RNAi) samples (d,e), most transcripts adjust to the predicted behavior of NB-expressed transcripts. (f) Venn diagram of the number of transcripts filtered out by this filtering step in irradiated (green) and Smed-H2B(RNAi). The relatively small P-value indicates that the overlap is significant. Transcripts filtered out by any of the filters were discarded in the other dataset as well. (g) Smed-H2B(RNAi) IS versus irradiation IS plot of the 823 transcripts not filtered out. Most of the transcripts are distributed above the diagonal, indicating that their Smed-H2B(RNAi) insensitivity (IS) is higher than their irradiation IS.
Solana et al. Genome Biology 2012 13:R19 doi:10.1186/gb-2012-13-3-r19