GSM8501043: mouse neuron nuclei, 50000 cells, Replicate 4, Hi-C; Mus musculus; Hi-C
Hi-C libraries were prepared using FLIE Hi-C protocol. Cells were crosslinked with 2% formaldehyde. The cells were lysed in cold lysis buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630) to permeabilize the nuclei. The nuclei were digested with DpnII restriction enzyme, following by end-filling with biotin-14-dATP, dCTP, dGTP, and dTTP with Klenow. Blunt ends were ligated with T4 DNA ligase, and the formaldehyde crosslinking was reversed by proteinase K (10 mg/ml). DNA was purified using phenol-chloroform and ethanol precipitation, sonicated to an average size of 200 bp, and biotin was removed from non-ligated DNA ends with T4 polymerase. Biotinylated chimeric DNA strands were pulled down using streptavidin beads (Dynabeads C1). Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's instructions.