Verification of specificity. Microarrays were printed with 1816 oligonucleotides in duplicate. Each sub-grid has 13 columns and 8 rows. (A) SYTO59 DNA staining demonstrating the layout of one sub-grid. The spot in the upper right corner and the spot four columns to the left were printed with Cy3-labeled oligonucleotides for orientation purposes. Some positions near the top of each sub-grid were printed with buffer only, and are thus not visible on SYTO59 staining. (B)-(F): cDNAs contain the complementary strand of one of the 50mers on the array were amplified by PCR and labeled with Cy3. Hybridization of these cDNAs to the microarray shows that only the complementary spot had fluorescent signal in most cases. cDNA for Rn.2401 also hybridized to another spot in the same sub-grid, but with lower intensity.