Protocol for performing ATAC-seq on nuclei isolated from Drosophila melanogaster stage 5 embryos that were flash frozen and then cut in half along the anterior-posterior midline. Data from this protocol are presented in the following paper: https://www.biorxiv.org/content/early/2017/09/27/195073.This protocol is based adapted from the following sources: https://www.nature.com/nmeth/journal/v10/n12/full/nmeth.2688.html and http://journals.plos.org/plosgenetics/article?