"We used miRDeep2 (Friedlander et al. 2012) using miRNA sequences downloaded from miRBase (Kozomara and Griffiths-Jones 2011) to quantify the levels of miRNAs in infected versus uninfected animals... Down-regulated miRNAs included the abundant miRNAs miR-71 and miR-80, which we confirmed via qPCR (Supplemental Fig. 6)."