Capsicum annuum 350k Microarray Expression profiling was conducted with the Capsicum annuum 350k Microarray. The 350k Microarray was designed from 29,580 unigenes. Among these, the direction of 24,417 was known and 6 probes for each gene were designed and duplicated in 2 blocks. The direction of 5,163 genes was not known and designed 6 probes for sense and anti-sense direction, respectively. In total, 350,000 probes were designed. The average size of probe is 60-nt long with adjusting its Tm value 75 to 85 °C. The microarray was manufctured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (48,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image. To assess the reproducibility of the microarray analysis, we repeated the experiment two or three times with independently prepared total RNA. The normal distribution of Cy3 intensities was tested by qqline. The data was nomalized and processed with cubic spline normalization using quantiles to adjust signal variations between chips and Rubust Multi-Chip Analysis (RMA) using a median polish algorithm implemented in NimbleScan (Workman et al., 2002. Genome Biol. 3: research0048.1 - research0048.16 ; Irizarry et al., 2003. Nucleic Acids Research 3:e15). Hybridization Genes on microarray