Two independent biological replicates used.
Chromatin was immunoprecipitated using rabbit anti-Doc2 antiserum (FBrf0160877). Since Doc2 and Doc3 have almost identical expression patterns and are functionally redundant, the two proteins are expected to occupy the same sites.
Chromatin was prepared from formaldehyde-fixed embryos as previously described (FBrf0202481).
Immunoprecipitated chromatin was analyzed by Affymetrix GeneChip Drosophila Tiling 1.0R array
Peaks were called with TileMap software (v1) after quantile normalization. For each enriched region, probe intensity peaks were identified as extrema on a smoothed curve of the log2-ratio signal. Finally, 200 bp regions centered on identified extremas were defined. Peak calls were lifted over from Dmel_Release_5 to Dmel_Release_6 using the NCBI Genome Remapping tool.
