HiC of OCT4-Mu without SKM  biological replicate 2
The DNA fragments were eluted off the beads in 300ul of Tris-buffer. To isolate biotin-labelled ligation junctions, 30ul of 10 mg/ml Dynabeads MyOne Streptavidin T1 beads were washed with 400ul of 1Tween washing buffer (5 mM Tris-HCl pH 7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween 20), collected with a magnet, resuspended in 300ul of 2 binding buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 2 M NaCl) and added to the sample. Biotinylated DNA was bound to the beads by incubating the sample for 15 min at room temperature. For end-repair , resuspend the DNAs-on-Dynabeads in 100ul mix: 10ul NEB T4 DNA ligase buffer, 5ul dNTP  mix, 5ul T4 PNK, 4ul T4 DNA polymerase I, 1ul DNA polymerase I, large (Klenow) fragment, 75ul water were add to incubate for 30 min at 37C. Resuspend the DNAs-on-Dynabeads in 100l of master mix: 10l NEB buffer 2, 5l 10mM dATP, 5l of 10U/l NEB Klenow exo-(NEB, M0212), 80l water for A-tailing. Shake at 900 r.p.m. for 30 minutes at 37C on the thermomixer. The adapter was ligated by incubating in a mixture of 25ul Quick Ligation Buffer, 2ul Quick Ligase, 3ul Illumina indexed adapter and 20ul water for 15min at room temperature. 2.5ul User Enzymewas added for further incubation 15min at 37C. Library preparation was performed with an NEBNext DNA Library Prep Kit, libraries were amplified for 10-12 cycles and were size-selected with Beckman AMPure XP beads. Two biological replicates were performed for each cell line.