Citrus 300k Microarray Expression profiling was conducted with the Citrus 300k Microarray. The 300k Microarray was designed from 4 major Citrus sperices: Citrus clementina, Citrus reticulata, Citrus sinensis, and Citrus unshiu. In total, 174,228 ESTs were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene) and clustered with CAP3 (http://genome.cs.mtu.edu/cap/cap3.html). Among 67,881 unigenes, the direction of 54,355 was known and 4 probes for each gene were designed. The direction of 13,682 genes was not known and designed 4 probes for sense and anti-sense direction, respectively. In total, 326,876 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