GSM5571572: EpiLC_ATAC_1; Mus musculus; ATAC-seq
ATAC-seq experiment was performed as described previously (Corces et al., 2017; Buenrostro et al., 2013) with minor modifications. We used FACs-sorted viable cells for mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs, d4 mPGCLCs, and d4c7 mPGCLCs, and FACS-sorted AAG-positive cells for GSCs and GSCLCs. 50,000 cells were permeabilized in cold lysis buffer 1 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin (Promega)) for 3 min followed by addition of 1 ml of cold lysis buffer 2 (10 mM Tris-HCl pH8.0, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween20). Nuclei were centrifuged and resuspended with a 50 ul of transposase reaction mixture (25 ul of 2xTD buffer (Illumina, 20034197), 2.5 ul of Transposase (Illumina, 20034197), 16.5 ul of PBS, 0.5 ul of Digitonin, 0.5 ul of Tween-20, 5 ul of DDW). After incubation at 37°C for 30 min, the tagged DNA was purified using the Minelute PCR purification kit (QIAGEN). The purified DNA was amplified 8 cycles by a PCR reaction (NEB, M0541S) followed by size selection using AMPure XP beads (Corning) to remove primer dimers.