112 Chapter 4 Figure 1: Effect of culturing conditions on the protein expression profile of macrophages. Alveolar macrophages were cultured on uncoated, globular collagen-coated or fibrous collagen-coated tissue culture plastic (n=6). a. Partial least squares-discriminant analysis plot of alveolar macrophages in the different conditions showing that the 3 conditions cluster separately. b. Heatmap of 77 proteins that were differentially expressed (p<0.025) between uncoated and collagen type I-coated conditions (fibrous and globular pooled). c. Heatmap of 142 proteins that were differentially expressed (p<0.05) between macrophages cultured on fibrous or globular collagen. Expressed as Log2 of the median values and statistically tested with an unpaired (b) or a paired (c) Wilcoxon test. We first investigated the effects of culturing macrophages on collagen versus uncoated plastic. Culturing macrophages on collagen type I-coated tissue culture plastic resulted in differential expression of 77 proteins compared to macrophages on uncoated plastic (Figure 1b and Supplementary Table 1). 69 of these proteins were more than 1.25-fold upregulated, whereas only three proteins were more than 1.25 fold downregulated (fold change >0.875) (Supplementary Table 1). To assess
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