Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen). Samples were mixed immediately by vortexing for 5 s, incubated for 5 min at room temperature, and then centrifuged at 5000g for 10 min. The supernatant was decanted and any residual supernatant was removed by inverting the tube once onto a paper towel. Total RNA samples were then isolated using RNeasy Plus Mini kit (Qiagen) following the manufacturer's instruction. Samples were then quantified using a NanoDrop 1000 spectrophotometer (Thermo Scientific) and quality of the isolated RNA was checked by running RNA 6000 Pico Kit using Agilent 2100 Bioanalyzer (Agilent). Paired-end, strand-specific RNA-seq library was prepared using KAPA RNA Hyper Prep kit (KAPA Biosystems), following the instruction (39 (link),40 (link)). Resulting libraries were analyzed on an Agilent Bioanalyzer DNA 1000 chip (Agilent). Sequencing was performed on a Hiseq 2500 sequencer at the Genomics Core facility of University of California, San Diego.