title: MNase-seq for GBM39 rep2
design: One million cells were washed by  calcium-free PBS and resuspended in 1 ml lysis buffer (10 mM pH 7.5 Tris-HCl,  10 mM NaCl, 3 mM MgCl2, 0.5% IGEPAL CA-630, 0.15 mM spermine, 0.5 mM  spermidine, with Roche EDTA-free complete protease inhibitor cocktail) on ice  for 5 min. After centrifugation, cell pellets were resuspended in 160 l  digestion buffer (10 mM pH 7.5 Tris-HCl, 15 mM NaCl, 60 mM KCl, 0.15 mM  spermine, 0.5 mM spermidine, with protease inhibitor cocktail) on ice. 0.004  Unit of micrococcal nuclease (NEB) in 40 l digestion buffer (with 5 mM  CaCl2) was added to the suspension and incubated at room temperature for 10  min. Digestion was halted by 200 l stop buffer (20 mM EDTA, 20 mM EGTA, 1%  SDS). DNA was then extracted, repaired by Fast DNA End Repair Kit (Thermo  Scientific), adenylated by Klenow fragment (NEB), ligated with TruSeq  adapters (Illumina) and amplified to make paired-end sequencing library.