Chromatin was prepared from formaldehyde-fixed embryos as previously described (FBrf0202481).
Chromatin immunoprecipitated DNA was analyzed by next generation sequencing.
Reads were aligned using bowtie. Input DNA or His3 ChIP DNA was used as control data. Peaks were called with MACS 220.127.116.11. Peak calls were lifted over from Dmel_Release_5 to Dmel_Release_6 using the NCBI Genome Remapping tool.