Fig. 4

E. tenella infection leads to a different macrophage response between conventional and GF chickens. A Differential gene expression was determined for 7 days post infected conventional versus (vs) non-infected conventional (left) and 7 days post infected GF vs non-infected GF (right) on volcano plots. Scattered dots represent each gene. Only significantly different gene expression (P < 0.05) and fold change > 2 or < − 2 are indicated. These thresholds are indicated with dashed lines on the plots. PTGS2 is underlined in red indicating that close significant up regulation. (B) Venn diagram showing differences and similarities in upregulated and downregulated genes in conventional and GF-infected chickens