title: Hi-C of D.virilis stage 15-16 embryos, replicate 2
design: Fly embryos were fixed for 15 min in 5 mL of 1 % methanol-free formaldehyde in PBS with 5 mL heptane while shaking. Embryos were re-fixed with 1 % methanol-free formaldehyde for 10 min at RT while breaking them into smaller fragments in a dounce homogenizer. Nuclei for in situ Hi-C were extracted from fixed fly embryos by resuspension in lysis buffer and sonication following the NEXON protocol (Arrigoni et al. 2015). Hi-C experiments were performed using a modified version of the in situ Hi-C protocol (Rao et al. 2014) described in (Ramrez et al. 2018). Nuclei were digested using DpnII. 50ng of DNA bound to beads was used for library preparation using a modified version of the NEBNext Ultra II DNA library preparation workflow and libraries were sequenced paired-end with a read length of 75bp. The average insert size is between 380-450bp.