RNA was isolated using RNeasy kit (Qiagen). Samples were incubated with lysozyme (0.5 mg/mL) for 15 minutes with agitation to lyse cells. Subsequent RNA isolation was performed according to the manufacturer's instructions. Genomic DNA was depleted using the Turbo-DNAfree Kit (Invitrogen). rRNA was removed using the NEBNext rRNA Depletion Kit (bacteria). Sequencing libraries were prepared using the xGen Broad-range RNA Library Prep (IDT) and xGen Normalase UDI Primer Plate 1 (IDT) according to the manufacturer's instructions.