title: ATAC-seq of Mus musculus hepatocellular carcinoma
design: ATAC was performed as described in Buenrostro et al.. Briefly, 50,000 cells were harvested and centrifuged (500 x g, 5 min, 4  C). Cells were washed in cold PBS and centrifuged (500 x g, 5 min, 4  C). Nuclei were isolated by resuspension of the cell pellet in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifugation (500 x g, 5 min, 4  C). Nuclei were subjected to tagmentation in 50  l reactions containing 1X TD buffer and 2.5  l T5 transposase followed by incubation at 37  C for 30 min. Tagmented DNA was recovered using a QIAGEN MinElute kit and eluted in 10  L Elution Buffer (10 mM Tris-HCl pH 8.0). Libraries were amplified for 14 cycles, purified using a QIAGEN PCR Cleanup kit and eluted in 20  l Elution Buffer. Size distribution of libraries was determined on a Bioanalyzer 2100 instrument.