Genome Scans were performed using NimbleGen HD2 arrays (NimbleGen Systems Inc) according the to the manufacturer’s instructions using a standard reference genome SKN1. NimbleGen HD2 dual-color intensity data were normalized in a two-step process: first, a “spatial” normalization of probes was performed to adjust for regional differences in intensities across the surface of the array; second, the Cy5 and Cy3 intensities were adjusted to a fitting curve by invariant set normalization, preserving the variability in the data. The log2 ratio for each probe was then estimated using the geometric mean of normalized and raw intensity data25.
