library_construction_protocol: RNA was isolated using the SV RNA isolation kit (Promega). 23S and 16S rRNA was depleted using a MicrobExpress kit (Ambion) and genomic DNA digested using amplification-grade DNase I (Invitrogen). RNA was reverse-transcribed using random primers (Invitrogen) and Superscript III (Invitrogen) at 45 °C for 3 h and denatured at 70 °C for 15 min. Nextera XT libraries were constructed and sequenced with over 30,000 reads per sample (min estimated coverage above x107).