Profiling the transcriptome response of Atlantic salmon to formalin-killed Renibacterium salmoninarum

Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify R. salmoninarum bacterin-responsive genes in Atlantic salmon, fish (n=6) were intraperitoneally injected with a high (5×107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum or phosphate-buffered saline (PBS control). Head kidney samples were collected at 24 h post-injection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to formalin-killed R. salmoninarum injection. Twelve Atlantic salmon were injected with a high (5×107 cells/kg; High-Rs) dose of formalin-killed R. salmoninarum or phosphate-buffered saline (PBS control) and head kidney samples were collected at 24 h post-injection. Test samples were labeled with Cy5, whereas the common reference (i.e. a RNA pool of all 12 samples included in microarray experiment) was labeled with Cy3. Each individual test sample was hybridized together with the common reference sample on an array (i.e. 12 arrays in total). variable: other: PBS: PBS1, PBS2, PBS3, PBS4, PBS5, PBS6. variable: other: High_Rs: High_Rs1, High_Rs2, High_Rs3, High_Rs4, High_Rs5, High_Rs6. repeat: biological replicate: PBS: PBS1, PBS2, PBS3, PBS4, PBS5, PBS6. repeat: biological replicate: High_Rs: High_Rs1, High_Rs2, High_Rs3, High_Rs4, High_Rs5, High_Rs6.