159807.fig.004
Figure 4: Comparison of the zebrafish innate immune response to different bacterial pathogens. Gene expression profiles of zebrafish embryos and adults infected with E. tarda FL6-60 (Et), S. typhimuriumSL1027(St), and M. marinum Mma20 (Mm) are depicted in a heat map. Embryos were infected with 200 CFU of each pathogen into the caudal vein at 28 hpf and snap frozen individually at 8 hpi for E.  tarda and S. typhimurium, and at 8 hpi and 4 dpi for M. marinum. Triplicate samples for each infection condition were compared with samples from control embryos (injected with PBS) using a common reference microarray design. The raw data were deposited in the Gene Expression Omnibus database under accession number GSE35474. The data derived from embryonic infections were compared with data from a study in which adult zebrafish were infected intraperitoneally with M. marinum Mma20, after which RNA samples were taken at 1 dpi and 6 dpi [22]. The dose of the Mma20 strain used in the adult infection study was lethal within days after the final sampling point at 6 dpi. Only genes relevant to this paper were included in the heatmap. All selected genes are represented by a minimum of two probes that showed significant up or downregulation (significance cut-offs for the ratios of infected versus control groups were set at 2-fold with ). Upregulation is indicated by increasingly bright shades of yellow, and downregulation is indicated by increasingly bright shades of blue. It should be noted that the genes listed in this figure are named according to sequence homology with mammalian counterparts and in most cases have not yet been confirmed functionally.