ChIP-seq experiments were performed as described (He et al 2011, Nature Genet, He et al 2015, Nature Biotech) with the following differences: ~100 mg embryos were used per IP. After incubation of magnetic beads with antibodies, H3K27ac IP samples were washed 3 times by rotating tubes for 3 min at 4°C to reduce background. Several different methods were used for library construction, please refer to the supplemental material of Koenecke et al 2016, Genome Research or Koenecke and Johnston, 2016, Genome Biol