Small RNA sequencing of HCV infected hepatoma cells

HCV infection requires both virus and host factors, including endogenous genes, a large proportion of which are noncoding RNAs (ncRNAs). The identification and mechanistic elucidation of these stably and conservatively expressed RNAs will shed light on HCV gene diagnosis and therapy. Nevertheless, most studied ncRNAs in HCV are microRNAs, with numerous other types of ncRNAs being neglected, such as long noncoding RNAs (lncRNAs) or small nucleolar RNAs (snoRNAs). Here, using two different hepatoma cell lines, we performed small RNA sequencing and analyzed the differential expression of microRNAs and snoRNAs, which provide data for further functional validation of snoRNAs and microRNAs during HCV infection. Huh7 and Huh7.5.1 cells were infected with JFH-1 HCVcc, and total RNA was extracted at specific time points (0, 6, 24, and 48 h) postinfection using TRIzol reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s instructions for transcriptome sequencing. For small RNA sequencing, 10 μg of total RNA for each sample was used for small RNA cDNA library preparation, and microRNA and snoRNA were mapped and analyzed.