Figure 1.

Chronic T. gondii infection stimulates a dramatic shift in gene expression as infection progresses from early to late chronic stages. (A) Heat map of all genes from merged Neuropathology, Neuroinflammation, and InflammationPLUSCustomCodeset panels. Gene expression depicted from low expression (blue) to high expression (orange). Heat map generated from normalized gene expression data using nSolver software. (B) PCA plot of biological replicates at all time points. Numbers on axes represent percentage of variation in that component. (C) Differential expression analysis results of 14 dpi, 28 dpi, and 56 dpi compared to Naïve control values demonstrates the majority of genes as upregulated. Top 25 genes most significantly upregulated identified based on fold change (x-axis) vs. p-value (y-axis). Four adjusted p-value cutoffs in each plot are as follows from bottom (dashed line) to top (solid line): <0.50, <0.10, <0.05, <0.01. (D) Table of 10 most significantly upregulated genes at each time point (from C.) Numbers in parentheses represent fold-change of gene. (E) Overlap between differentially expressed genes plotted in (C). Numbers and percentages in diagram based on genes significantly upregulated with adjusted p-value cutoff <0.05.