title: Hi-C of D.busckii stage 15-16 embryos, replicate 2, sequencing run 2
design: Fly embryos were 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. Dangling ends were removed using T4 DNA polymerase. 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 library insert size is between 380-450bp.