GSM2771829: rng-interrupted mutant 15 min; Stenotrophomonas maltophilia; RNA-Seq
RNA was extracted every 5 min after rifampicin addition. Five ml samples obtained at any given time were spun down for 20 min at 6,000xg, 4°C and pellets were immediately frozen on dry ice and stored at −80°C. Total RNA was extracted and cleaned up using the RNeasy mini-kit (Qiagen). Duplicated RNAs from each strain and each time point were pooled. RNA samples (3,5 µg each) were rRNA depleted with RiboZero (Epicentre). RNA was then subjected to RNA library prep using the Ultra Directional RNA Library Prep Kit (Cat no. E7420S, New England Biolabs) following manufacturer recommendations. Libraries were pooled and fragments with lengths between 200 and 500 bp were purified from agarose gels. Remaining adaptor dimers were cleaned with AMPure XP beads (Beckma-Coulter). Libraries were sequenced in a Miseq system (Illumina) using a v3 cartridge and a 150 bp, single-read format at the Parque Científico de Madrid.