title: GSM5344536: HiChIP in zebrafish ctcf mutant embryos at 48hpf, replicate 2; Danio rerio; OTHER
library_construction_protocol: Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for HiChIP preparation as previously described (Mumbach et al. 2016). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. Chromatin was sonicated in a Covaris M220 sonicator for fragments around 300 bp and immunoprecipitated with anti-H3K4me3 (abcam). DNA was extracted after cross-link reversal and biotinylated products were recovered with streptavidin-coated beads, TAGmented with Tn5 transposase and purified for library preparation. Preparation of HiChIP libraries was performed as described for ATAC-seq assays in Buenrostro et al., 2015