Effect of decreased sequencing depth on detection of differentially expressed genes by RNA-Seq. Differentially expressed genes were identified by DESeq with P < 10-3. A) Comparison of EDL933 gene expression in exponential and stationary phase. The total number of aligned non-rRNA fragments in these datasets ranged from 25-30 million. B) Comparison of V. cholerae gene expression in minimal media and the rabbit cecum. The total number of aligned non-rRNA fragments in these datasets ranged from 4-6 million.