GSM6858877: In vitro haustoria, Dcp-treated RNA, replicate 1; Cuscuta campestris; ssRNA-seq
Total RNA was extracted using the Zymo Quick-RNA Plant kit per the manufacturer's instructions. Each RNA was treated in 3 different ways: Dcp ("Decapping Enzyme" from NEB), RppH (NEB), or no treatment, thus producing the nine samples. After treatments, libraries were constructed using a splint-ligation protocol as described for microRNAs by Maguire et al. (10.1093/nar/gkaa480) except that no size-selection was performed. The resulting libraries include full-length, stranded RNAs between ~10 and ~400 nts in length. The libraries require a 5' monophosphate, so that the abundance in the Dcp or RppH treatments can give an indication as to the identity of the in vivo 5'-ends. Specifically, RNAs enriched in both RppH and Dcp are likely capped, while RNAs enriched only in RppH are likely 5'-ppp.