title: GSM4724552: HiC in zebrafish ctcf mutant embryos at 48hpf, replicate 1; Danio rerio; Hi-C
library_construction_protocol: Embryos were fixed in 1% paraformaldehyde and quenched with 0.125M Glycine. Cell were lyses and extracted nuclei were processed for in-situ HiC preparation as previously described (Rao et al. 2014). Briefly, chromatin was digested with DpnII, fragment-ends were blunted and marked with dATP-biotin, followed by proximity ligation. DNA was extracted after cross-link reversal and sonicated in a Covaris M220 sonicator for fragments between 150-600 bp. Proximity ligation products were enriched using Streptavidin-coated beads. End-repair, A-tailing and ligation of TruSeq indexing adapters followed standard procedure for Illumina library preparations for paired-end sequencing. Final library was prepared using NEBNext High-Fidelity 2X PCR Master Mix (NEB) and standard TruSeq Primer 1.0 (P5) and TruSeq Primer 2.0 (P7).