Whole Transcriptome Sequencing
Total RNA was isolated from both C (control) and T (CIP treated cells) bacterial samples using standard TRIzol (Thermo Scientific, USA) based method with minor modifications. The qualities and quantities of the isolated RNA samples were checked on 1% denaturing agarose gel and NanoDrop (SPECTROstar Nano BMG Labtech), respectively. After quantification paired-end, RNA-seq sequencing libraries were prepared from the purified RNA samples using Illumina TrueSeq mRNA sample Prep kit (Illumina, U.S.) and MICROBExpress kit (Invitrogen, USA) as per the manufacturers protocol. In brief, at first total mRNA was enriched from the extracted total RNA using a MICROBExpress kit. The enriched mRNA was then reverse transcribed to 1st strand cDNA using random hexamer and superscript III reverse transcriptase followed by second strand conversion using second strand mix. Finally, the double-stranded cDNA was purified using AMPure XP beads (Beckman Coulter, U.S.) and then fragmentation was done using Covaris M220 to generate a mean fragment distribution of 350 bp. The fragments were subjected to end-repair using an end repair mix followed by an adenine (A) tailing, adapter ligation, and then enriched by a limited number of PCR cycles. After the library preparation, QC-passed libraries were sequenced on the Illumina platform using 2 X 150 bp chemistry