Labeling and hybridizing the DNA

Once the required amount of DNA (1-2 ^g) has been obtained for both the antibody ChIP sample and the no-antibody control, it is labeled with the fluorescent Cy5 and Cy3 dyes. There are several commercially available DNA labeling systems for incorporating these dyes into the DNA samples. Once the labeled samples have been obtained, DNAs are cohybridized to the selected microarray. Following hybridization, the arrays are washed, scanned and analyzed like other types of microarray. Many institutions have established core-facility units specialized in microarray hybridization and it is advisable to use their expertise during the analysis.

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