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search for strain-specific differentially expressed genes, we performed comparisons of gene expression between the DBA/1 and FVB/N strains at all four phases of CIA, including NC, PI, OA and CA. For the naive mice without immunisation, 361 genes were differentially expressed between the two strains. On day 10 after immunisation, when both strains did not show any sign of the disease, 141 genes were differentially expressed. After DBA/1 mice developed CIA, 184 and 85 differentially expressed genes were identified between these two strains at the onset and chronic phases, respectively. When the lists of the differentially expressed genes at the four phases were merged and overlapping genes were excluded, 509 genes were identified (Additional file 1). Twenty-one genes consistently showed differential expression between the two strains at all phases. Besides these 21 genes, only 3 additional genes were strain-specific differentially expressed during the 3 phases after CIA induction (PI, OA and CA; Figure 1)."}

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