Differential Expression (DE)
We created a gene-level read count matrix for all samples usingfeatureCounts (Liao et al., 2014). The read count matrix was filtered for a minimum count cutoff = 3 cpm over at least two replicates per comparable group. All DE analyses were performed using the R packageedgeR (Robinson et al., 2009) after TMM library normalization. Normalized read counts were analyzed by Generalized Linear Models (GLM) assuming a negative binomial model of read counts. All comparisons were performed using a full factorial design that included parental and offspring acclimation treatments using three biological replicates. Transcriptional TGP was assessed by comparing samples whose parents were acclimated at 36 °C vs 25 °C, while WGP was detected by comparing relative expression changes between offspring samples acclimated at 36 °C vs 25 °C. Genes with a false-discovery rate (FDR) corrected p-value of < 0.05 (Benjamini and Hochberg, 1995) and a log2-fold-change threshold of > 1.0 were considered significant. A correlation matrix comparing relative expression levels of significant DE genes was then generated in order to investigate the relationship between transcriptional WGP and TGP.