Brassica napus 300k Microarray Expression profiling was conducted with the Brassica napus 300k Microarray. The 300k Microarray was designed from 80,696 unigenes clustered from 543,448 ESTs and 780 cDNA at NCBI (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene). Four 60-nt long probes were designed from each gene starting 60 bp ahead the stop codon and with shifting 25 bp so 4 probes cover 150 bp in the 3’ region of the gene. Among these, the direction of 67,165 was known and 4 probes per gene were designed. The direction of 27,944 genes was not known and designed 4 probes starting 250 bp ahead from the end of the unigene and covered 150 bp downstream. For these unknown genes 4 probes were designed for sense and anti-sense direction, respectively. In this way, 341,853 60-nt long probes were extracted in total. Genes from chloroplast (6), mitochondria (103) and selection marker genes such as gfp, gus, hyg, bar, and kan are included. The average size of probe is 60-nt long with adjusting its Tm value 75 to 85 ℃. The microarray was manufactured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (40,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image. Hybridization Genes on microarray