Transcriptome from Trichobranchus roseus
Tissue was either finely chopped, placed in RNAlater (Ambion) for 24 h at 4C and then stored at -80C or -20C, or it was flash-frozen in liquid nitrogen and stored at -80C. Total RNA was extracted from Trizol (Ambion) using Direct-zol RNA kits (Zymo Research) including a DNase I digest to remove genomic DNA following the manufacturers specifications. mRNA was purified with a  Dynabeads mRNA Direct Micro Kit (Invitrogen). Quantity and quality of mRNA was assessed with a Qubit fluorometer (Invitrogen) and Tapestation RNA Screen Tape (Agilent). Libraries were prepared using KAPA Stranded mRNA-Seq kits (KAPA Biosystems) following the recommended protocol and using custom 10 nucleotide Illumina TruSeq style adapters [29]. Libraries were sequenced on the Illumina HiSeq4000 using 100 base pairs paired end reads at the IGM Genomics Center (University of California San Diego).