Methodological considerations are shown with respect to the two-phase study design. Using microarrays, RNA from irradiated and nonirradiated baboon samples was hybridized and gene fluorescence intensity per gene (dot) compared (panel A). A significant fold change as shown was used as a filter to identify candidate genes, which were forwarded for validation using qRT-PCR. Using next generation sequencing (NGS) in the context of another project, we identified radiation-induced “exon driver regions” and exon regions predominantly contributing to the baseline gene expression level (panel B, left side). Panel B (right side) reflects the agreement of differential gene expression measured in microarrays (baboons) and qRT-PCR. The low-density arrays (LDA) were loaded with three technical replicates (indicated by different symbols and colors) and expected overlap of replicate measurements is shown between 15–30 raw Ct values (threshold cycle), but not afterwards where technical replicate measurements vary over a wide range of raw Ct values (panel C). This procedure allowed defining of the linear-dynamic range as well as the range where measurements are reproducible and convert into quantitative values.