Comparative transcriptome analysis by RNAseq of necrotic enteritis Clostridium perfringens during in vivo colonization and in vitro conditions

Table 1 The number of significantly differentially expressed genes (DEGs) in NE-strain CP1 under different growth conditions

Growth Conditions¹		edgeR² number of genes	UpRegulated³	DownRegulated³
in vivo	IV x RM	673	387	286
	IV x PM	382	148	234
	IV x OS	521	376	145
in vitro	PM x RM	600	441	159
in vitro	OS x RM	196	44	152

¹ RM: rich medium, PM: poor medium, OS: osmotic shock
²egdeR: logFC: ≥2-fold differences in the transcript abundance plus ≤1 % false discovery rate (FDR)
³Number of genes up- or downregulated