Transcriptomic profiling of the adaptive and innate immune responses of Atlantic salmon to Renibacterium salmoninarum infection

Renibacterium salmoninarum is a Gram-positive, intracellular bacterial pathogen that causes Bacterial Kidney Disease (BKD) in Atlantic salmon (Salmo salar). To identify Atlantic salmon genes responsive to R. salmoninarum pathogen, fish were intraperitoneally injected with R. salmoninarum (BKD) or sterile KDM-2 medium (control). Head kidney samples were collected at 13 days post-infection. Using 44K microarray analysis, transcriptome analysis was performed to identify differentially expressed probes in response to different levels of R. salmoninarum infection. Atlantic salmon (54 ± 6 g) in the BKD group were injected with live R. salmoninarum, whereas fish in the control group were injected with sterile KDM-2 medium. The head kidney samples were collected at 13 days post-infection. The infection level of samples was determined using a TaqMan qPCR assay, and fish (n=5) with no (Control), high (H-BKD) or low (L-BKD) infection level were subjected to microarray analyses. Test samples were labeled with Cy5, whereas the common reference (i.e. a RNA pool of all 15 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. 15 arrays in total). variable: Control: Control1, Control2, Control3, Control4, Control5. variable: L-BKD: L-BKD1, L-BKD2, L-BKD3, L-BKD4, L-BKD5. variable: H-BKD: H-BKD1, H-BKD2, H-BKD3, H-BKD4, H-BKD5. biological replicate: Control: Control1, Control2, Control3, Control4, Control5. biological replicate: L-BKD: L-BKD1, L-BKD2, L-BKD3, L-BKD4, L-BKD5. biological replicate: H-BKD: H-BKD1, H-BKD2, H-BKD3, H-BKD4, H-BKD5.

杀鲑肾杆菌（Renibacterium salmoninarum）是一类革兰氏阳性（Gram-positive）胞内细菌病原体，可引发大西洋鲑（Salmo salar）罹患细菌性肾病（Bacterial Kidney Disease, BKD）。为鉴定大西洋鲑中响应杀鲑肾杆菌病原体的差异表达基因，研究人员对试验鲑鱼腹腔注射杀鲑肾杆菌（BKD组）或无菌KDM-2培养基（对照组），并于感染后13天采集头肾样本；采用44K微阵列开展转录组分析，以筛选响应不同感染水平杀鲑肾杆菌的差异表达探针。

本试验所用大西洋鲑体重为54±6 g，BKD组注射活杀鲑肾杆菌，对照组注射无菌KDM-2培养基，两组均于感染后13天采集头肾样本。通过TaqMan定量聚合酶链反应（qPCR）测定样本感染水平，最终选取无感染（对照组）、高感染（H-BKD）与低感染（L-BKD）水平的个体各5尾（n=5）进行微阵列分析。待测样本以Cy5标记，通用参考样本（即本微阵列实验中全部15个样本的RNA混合池）以Cy3标记；每个待测样本均与通用参考样本共同杂交至芯片上，本次实验共计使用15张芯片。

变量分组如下：
对照组变量：Control1、Control2、Control3、Control4、Control5；
低感染组（L-BKD）变量：L-BKD1、L-BKD2、L-BKD3、L-BKD4、L-BKD5；
高感染组（H-BKD）变量：H-BKD1、H-BKD2、H-BKD3、H-BKD4、H-BKD5。

生物学重复分组如下：
对照组生物学重复：Control1、Control2、Control3、Control4、Control5；
低感染组生物学重复：L-BKD1、L-BKD2、L-BKD3、L-BKD4、L-BKD5；
高感染组生物学重复：H-BKD1、H-BKD2、H-BKD3、H-BKD4、H-BKD5。