Detection of gene expression changes in S. Choleraesuis infected porcine lung using an oligonucleotide microarray

Piglets were raised in isolation facilities from 10 days to 7 weeks of age at the National Animal Disease Center. Bacteriological culture of rectal swabs was performed twice to confirm that all pigs were free of Salmonella spp. Three control pigs were necropsied on experimental day -3. On day 0, pigs in the infected group were intranasally challenged with 1 x 109 CFU S. Choleraesuis X3246. Lung samples were aseptically collected from three 24 h and three 48 h post infection pigs and immediately frozen in liquid nitrogen for future mRNA isolation. In the microarray experiment, the nine animals were randomly assigned to three loops so that each loop included one animal from each infection status category. A total of 9 slides (3 slides per loop) were used to obtain a total of 18 measurements from the three control and six infected pigs. A mixed model analyses was also used to identify differentially expressed genes. The mixed model included fixed effects for dye (Cy3 or Cy5), time point (control, 24 hour, and 48 hour infection) as well as random effects for slide and animal. Keywords: repeat sample