title: Mnase-seq-mES_TIR1_ARID1A_mAID_0h_auxin rep_2_Run1
design: Cells were crosslinked with 1% formaldehyde for 10 min and quenched for 5 min with 125 mM glycine at room temperature. After washing cells with cold PBS, cells were lysed using cold NP40-lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.5% NP40, 0.15 mM spermine, 0.5 mM spermidine) for 5 min on ice. Cells were pelleted and washed with MNase digestion buffer (10 mM Tris pH 7.5, 15 mM NaCl, 60 mM KCl, 1 mM CaCl2, 0.15 mM spermine, 0.5 mM spermidine) and resuspended in 50 l MNase digestion buffer. For the digest, 7.5 units MNase S7 (Roche) were added to ~4 x 106 cells and incubated for 14 min at 37C. The digest was stopped adding 1/10 vol 10% SDS and 1/10 vol 250 mM EDTA. 0.24M NaCl and 10 g RNase A was added to reverse the crosslinking at 65C for 2 hrs. The samples were treated with 20 g proteinase K overnight at 65C, followed by phenol-chloroform extraction and purification using NEB Monarch PCR purification kit.