Fig. 2

Transcriptome analysis of E. faecium E745. Coverage plots of RNA-seq data aligning to chromosome and plasmid DNA are shown in panel a. The y-axis of each track indicates reads coverage and is represented on a log scale, ranging from 0 to 10,000. The x-axis represents the genomic location. Light blue (BHI) or orange (serum) tracks correspond to sequencing reads aligned to the plus strand of the replicon, and dark blue (BHI) or dark red (serum) tracks correspond to sequencing reads aligned to the minus strand of the replicon. The grey track corresponds to multi-gene operons. The green track corresponds to differentially expressed genes (BHI vs serum), with the height of the green bars indicative of differential expression. In panels b and c, two serum-induced regions are shown, i.e. a gene cluster involved in nucleotide biosynthesis (panel b) and a prophage (panel c). The RNA-seq experiments were performed using three biological replicates