"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)."
"...We measured gene induction during exposure to live S. aureus, which causes pathogenesis, or heat-killed S. aureus, which does not (Figures 3G-I and S4C, E). Unexpectedly, all 10 biomarker genes were induced at least equally well on heat-killed S. aureus as on live S. aureus (Figure 6A)."
Query-target gene pairs were tested for interaction by feeding target gene RNAi to worms with a mutation in the query gene. Each query-target pair and its two controls were tested in at least three rounds.|Target genes were classified as either belonging to LGIII (L) or to signalling pathways (S) or to both (L,S): S