Cy3 (input DNA) and Cy5 (immunoprecipitated DNA) dyes. Labeled input and immunoprecipitated samples were both hybridized to the same 2007-02-27_MM8_CpG island_promoter array (described below) as a two-color experiment and scanned using Nimblescan. The signal intensities for input DNA and immunoprecipitated DNA were used to calculate the ratio of IP/Input DNA.
