Cells equivalent to 50 OD600 units were collected and RNA was isolated using Tri-reagent. DNA contamination was reomved by TurboDNase treatment and RNA was cleaned afterward using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed by custom biotinylated oligos. Binding to magnetic streptavidin-beads removed rRNA. Efficiency of the depletion was verified by Bioanalyzer.  doi.org/10.1128/mBio.00010-20 The rRNA depleted RNAs samples were fragmented using magnesium fragmentation module (NEB). cDNA was synthesized by using the NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (NEB) following the manufacturer's instructions. cDNA libraries were column-based purified and cleaned left-sided using the Agencourt AMPure XP kit (Beckman Coulter Genomics). The quality and quantity of cDNA libraries was measured by Bioanalyzer and Qubit, respectively.