Figure 1. Experimental design used to investigate the effect of acclimation at 36 °C vs. control treatments at 25 °C in parents (P) and F1 offspring. Acclimation treatments in the parental generations were performed on adult stages, while offspring acclimation was performed on either larva or adult samples. All samples for RNA-Seq were collected in the offspring generation as a result of the four different combinations of acclimation treatments. The parental effect was used to assess transcriptional transgenerational plasticity (TGP), while the offspring acclimation was used to estimate within-generation plasticity (WGP).
We sequenced nearly 400 million paired-end Illumina reads across the 24 RNA-seq libraries. Of these, an average of 17 million reads per library mapped to the reference genome following trimming and filtering of sequence reads. An independent read-count matrix for each gene feature was generated (i.e., exons, junctions, introns, and gene-wide). All relative changes of transcriptional plasticity were estimated by comparing read counts between acclimated samples at 36 °C and control samples at 25 °C as performed in the parental or offspring generations (Figure 1).