Solanum lycopersicum 500k Microarray Solanum lycopersicum 500k Microarray. The 500k Microarray was designed from 45,071 unigenes clustered from 250,954 ESTs at NCBI (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene). Ten 60-nt long probes were designed from each gene starting 60 bp ahead the stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3’ region of the gene. Among these, the direction of around 34,000 was known and 10 probes per gene were designed. The direction of 10,000 genes was not known and designed 10 probes starting 250 bp ahead from the end of the unigene and covered 150 bp downstream. For these unknown genes 10 probes were designed for both sense and anti-sense direction, respectively. In total, 540,000 probes were designed. Selection marker genes such as gfp, gus, hyg, bar, and kan were 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