The transcriptional profile of intracellular P. salmonis

The transcriptional profile of intracellular P. salmonis was determined using a whole-genome microarray. Our microarray contained 5,309 different probes targeting 2,850. In our experimental design, the gene expression profile obtained from intracellular P. salmonis was compared with the transcriptome of control bacteria grown in culture medium. RNA from P. salmonis and SHK-1 cells were extracted simultaneously to avoid changes in transcriptomic profile after the bacterial purification process and eukaryotic RNA was depleted using the MicrobEnrich Kit. Two-condition experiment. For each condition studied, three independent biological replicates were analyzed for each condition (intracellular P. salmonis/P. salmonis grown in culture medium). Statistical analysis (adjusted p value<0.05) combined with a 2-fold variation cut-off indicated that 966 genes were differentially expressed at 12 days post-infection. Of these, 497 genes demonstrated increased expression while 469 genes were down-regulated.