Ruler Arrays Reveal Haploid Genomic Structural Variation

A ruler array combines novel sample preparation protocols, tiling genomic microarrays, and a new computational method to turn each probe on a microarray into a ruler that measures the physical distance between defined genomic sequences regardless of the intervening sequence. The ruler array protocol involves (1) genomic DNA purification (2) digestion with a restriction enzyme (3) ligation of a biotinylated adapter molecule to the cut sites (4) purification on streptavidin beads (5) polymerase extensions from a primer complementary to the adapter using labeled dNTPs and (6) hybridization to a tiling microarray Two replicates of our ruler array experiment to detect insertions and deletions between two genomic samples of strains FY4 and Sigma1278b.