Arabidopsis thaliana385k Microarray The 385k Microarray was desined from 30,387 genes. Six probes per gene was designed and duplicated in 2 blocks. The microarray was manufctured at NimbleGen inc (http://www.nimblegen.com/). 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