Supplementary Material for: Gene Expression Profiles in Murine Influenza Pneumonia

<i>Background:</i> Many in vitro studies have focused on gene expression in influenza-infected leukocytes, lung tissue or cell lines. However, knowledge of in vivo gene expression in these compartments is limited. <i>Methods:</i> To obtain insight into gene expression profiles during influenza infection, we determined the expression of multiple genes by using a newly developed mouse-specific multiplex ligation-dependent probe amplification assay. <i>Results:</i> The genes involved in inflammation, Toll-like receptor signaling, coagulation, fibrinolysis, cell adhesion, tissue repair and homeostasis were measured in lung tissue, leukocytes in bronchoalveolar lavage fluid and tracheal epithelial cells in mice, before and after intranasal infection with influenza A. Most of the genes investigated were differentially expressed during the course of infection and returned to baseline levels when mice had recovered from the infection. However, expression of several genes remained altered even though mice had completely cleared the virus. <i>Conclusion:</i> These data provide the first information on compartmentalized gene expression profiles in the respiratory tract during influenza.