WHAT KIND OF CONTROL PROBES DO I NEED TO INCLUDE IN THE CUSTOMARRAY DESIGN FOR HYB & SEQ?
For each assayed nucleotide position, the chips will have four identical probes with the 5′ termini variable (A,G, T or C) . One variant will be the wild-type oligonucleotide, one the mutation (e.g. known SNP) and the remaining two will be mismatches. These mismatches should not hybridize with the probe and can therefore be used as controls for background. Sequencing chips will also have four probes ending in the four nucleotides A, C, T, and G.
