Chromatin was prepared from formaldehyde-fixed embryos as previously described (FBrf0202481).
Two independent chromatin immunoprecipitations (ChIPs) were performed using two independent anti-Mef2 antibodies raised against residues 1-294 (FBrf0193172), and compared to two independent mock ChIPs using rabbit pre-immune sera, as previously described (FBrf0202481).
Immunoprecipitated chromatin was analyzed by Affymetrix GeneChip Drosophila Tiling 1.0R array