GSM4743408: ATAC.MK_2; Mus musculus; ATAC-seq
Three days after HDTV, livers were processed according to the Liver Dissociation Kit (Miltenyi Biotec). Immune cells were magnetically depleted using the MACS system and CD45 MicroBeads (Miltenyi Biotec). 40.000 RFP+ cells were facs sorted using a BD FACSAria™ III Cell Sorter.  Cells were washed in cold PBS and centrifuged (4000rpm, 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. Nuclei were subjected to tagmentation in 50 µl reactions containing 1× TD buffer and 2.5 µl T5 transposase followed by incubation at 37 °C for 30 min. Tagmented DNA was recovered using a QIAGEN MinElute kit and eluted in 10 µl elution buffer (10 mM Tris-HCl, pH 8.0). Libraries were amplified according to Buenrostro et al., 2015, purified using a QIAGEN PCR Cleanup kit and eluted in 20 µl elution buffer.