Embryos were collected, fixed in formaldehyde, and stored at -80 according to Blythe and Wieschaus, 2015, Chromatin immunoprecipitation was performed using Rabbit anti CLAMP or Rabbit IgG as described in Reider et al., 2017 Libraries were synthesized using 4ul of inputs and 36ul of each ChIP sample (Rabbit anti CLAMP or Rabbit IgG; Millipore-Sigma, 12-370) according to Blythe and Wieschaus (2015). Briefly, libraries were made using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs), 12 samples pooled per lane, and sequenced on an Illumina HiSeq 2500 in 2×150-bp mode (Genewiz).