Patterns of transcript abundance assessed by quantitative real time RT PCR as a function of pneumococcal colonization. Validating the microarray data. Transcript abundance of (A) irg1, socs3, and ifit3 and (B) infa and infB was measured in mock infected and colonized mice using the original NALT RNA samples utilized for microarray analysis. These samples were collected from NALTs harvested within the first week of colonization. A second infection was established and RNA was isolated from NALTs of mock infected and pneumococcal colonized animals. Transcript abundance of ifit3 was measured in these samples (Ifit3*) (PANEL A). (C) A third infection time course was performed using mock infected, EJ1 (WT) colonized, and EJ5 (ply-) colonized mice. NALTs were isolated and the abundance of ifit3 transcript was assessed to determine to effect of pneumolysin on the Type I Interferon Response within the first week of colonization. Samples isolated on Days 1 and 3 post-colonization were not statistically different from each other using any of the primer sets. Therefore, they were combined into a single group. Open circles represent mock infected samples, closed gray circles represent EJ1 colonized samples, and black circles represent EJ5 colonized samples. Horizontal lines represent the geometric mean. p values were calculated using a 1-tailed Students T-test.