Nuclei were collected from homogenized embryos and sonicated. Protein-DNA complexes, which are in the supernatant after sonication and centrifugation, were isolated with antibodies corresponding to each ChIP experiment. Libraries were prepared from ChIP and input DNA using the NEBNext® DNA Library Prep Master Mix Set for Illumina® kit (#E6040) either following the manufacturer’s instructions, or with a modified protocol using biotin-labeled dATP (Chen et al., 2013).