Total RNA was extracted from biological triplicates (duplicates in the case of Pheromone and Starvation dauers) using either the Direct-zol RNA Miniprep kit (Zymo Research, R2050) following the manufacturer's protocol, including an on-column DNase I digestion step, or a standard Trizol extraction method for dauer larvae. mRNA libraries were prepared using the Illumina TruSeq Stranded mRNA kit.