"RNA Seq of Vibrio cholerae C6706: TfoXconst., CytR+": Sample EA349_D
Total RNA from 3 independent cultures of four V. cholerae strains grown to exponential phase (OD600 0.5-0.7) in LB medium at 37°C was extracted using mirVana miRNA isolation kit (Ambion). DNase treatment for removal of genomic DNA was performed using TURBO DNA free kit (Ambion). Detection of contaminating genomic DNA was carried out by performing PCR amplification with primers specific for 16S rRNA loci, and DNase treatment was repeated until no PCR products were detectable. DNA-free total RNA samples were purified using RNEasy Minelute kit (Qiagen). All kits were used as per manufacturers’ instructions unless described otherwise. Further processing of the samples was conducted by Eurofins (Louisville, USA) using a standardized Illumina RNA Sequencing pipeline. Briefly, RNA sample quality was determined using an Agilent 2100 Bioanalyzer and Qubit, before ribodepletion using a Ribo-Zero Magnetic kit (Epicentre) for Gram-negative bacteria. Sequencing was performed using a HiSeq2000 sequencer (Illumina) and 100bp paired end reads were obtained. 