GSM2108278: chrr_merr_KO_BL_rep2; Vibrio cholerae O1 biovar El Tor str. N16961; RNA-Seq
Total RNA was extracted from OD600=1.0, 500 µl cell culture by using TRIzol reagent according to the manufacturer’s instructions. After quality and quantity measurements of RNA by using 2100 BioAnalyzer, RNA was treated with RNase-free DNase I at a concentration of 1 U/µg to remove residual genomic DNA. In order to remove the rRNA, 2.5 µg total RNA was treated with Ribo-Zero™ bacterial rRNA removal kit  following the manufacturer instructions. The rRNA depleted RNA pellets obtained after the ethanol precipitation step was re-suspended in 10 μl of RNase free water. After that, RNA samples were fragmented using fragmentation buffer by using TruSeq mRNA Sample Preparation Kit . The cleaved short RNA fragments were used for the first-strand cDNA synthesis using random hexamer-primer, and then the second strand was synthesized by using DNA polymerase I and RNase H. The double strand cDNAs were purified with AMPure XP beads and eluted with resuspension buffer followed by 3’end adenine nucleotide addition. Finally, sequencing adaptors were ligated to the fragments and cDNA fragments were enriched by PCR amplification. Enriched cDNA libraries were used for cluster generation and sequencing. Paired-end sequencing of the two cDNA libraries (dark and blue-light exposed) of each wild type and mutant V. cholerae cells was performed using the Illumina MiSeq sequencing platform.  All sequence data are PE 2x75 bp.  Image processing, base calling, and quality calue calculation were performed by the Illumina data processing pipeline (v1.5). High quality reads were saved in FASTQ format.