Illumina HiSeq 2500 paired end sequencing
Random RNA sequencing
After cultivation, total RNA was purified from cell pellets using the Masterpure complete DNA & RNA purification kit (Epicentre) following the manufacturer's protocol. The RNA quality was then determined using a Bioanalyzer and a Prokaryote Total RNA Pico Chip (Agilent Technologies). 5µg total RNA was then used in Ribo-Zero rRNA Removal Kit (bacteria) (Epicentre) according to manufacturer instructions to remove ribosomal (r) RNA. rRNA-depleted RNA samples were ethanol precipitated, and analyzed on a Bioanalyzer using mRNA Pico Chips (Agilent Technologies). RNA-sequencing libraries were generated from rRNA-depleted RNA samples using the ScriptSeq Complete library prep kit (Illumina) in combination with library size selection using a Pippin Prep cassette (Sage Science). The size selected cDNA library was sequenced with MiSeq Reagent Kit v3 with 2×75bp read length over 150 cycles,