Fig. 2

TE expression in the Dcr2 mutant is perturbed but not uniformly shifted. A MA plots of individual TE families grouped by order (DNA, LINE, LTR) for midguts (top row) and ovaries (bottom row). The x-axis shows mean read counts normalized by the median of ratios (DESeq2-based normalization) and the y-axis shows log₂ fold-change in the Dcr2 mutant line. Families are colored according to their differential expression (red: enriched in mutant line; blue: depleted in mutant line; grey: not differentially expressed). The dotted line in the center of each plot represents the mean log₂ fold-change. B Gene set enrichment analysis (GSEA) results. The height of each bar represents the normalized enrichment score (NES), i.e., the relative, rank-based enrichment of the TE order compared to a random, equally sized, group of transcripts. P-values above or below the bars indicate the false discovery rate for the enrichment (red bars) or depletion (blue bars) in the Dcr2 mutant relative to the wild-type control. C Box plot of RT activity measured in midgut and ovary samples relative to SuperScript II (SSII). P-values shown above the graph were generated by pairwise comparisons within a linear mixed effect model using Wald’s test