GSM8012605: EpiSCs converted to ESCs ATAC-seq shBrd8 Day 6 Rep2; Mus musculus; ATAC-seq
Briefly, nuclei from 50,000 cells were extracted with lysis buffer (10 mM Tris-HCl pH 7.4 10 mM NaCl, 3 mM MgCl2, and 0.2% (v/v) IGEPAL CA-630).  Tagmentation reactions were performed by addition of 50 ul reaction mix of the TruePrep DNA Library Prep Kit (Vazyme, TD502) according to the manufacturer's instructions. DNA fragments were cleaned up using the MinElute PCR Purification Kit (Qiagen, 28004). ATAC-seq libraries were amplified with PCR for an appropriate number of cycles 17 and the sequence index was added by TruePrep® Index Kit V2 for Illumina (Vazyme, TD202). The amplified DNA libraries were purified using the VAHTS DNA Clean Beads (Vazyme, N411-02) and sequenced on an Illumina sequencer. ATAC-seq library was generated using the Tn5 enzyme from the TruePrep DNA Library Prep Kit V2 (Vazyme, TD501-02) as previously described (Buenrostro et al., 2013). Briefly, a total of ~50,000 cells were washed once with 50 μl of cold PBS and resuspended in 50 μl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630). The nuclei were centrifuged for 10 min at 500 × g at 4 °C, followed by the addition of 50 μl transposition reaction mix (25 μl TD buffer, 2.5 μl Tn5 transposase (Vazyme) and 22.5 μl nuclease-free water). Samples were PCR amplified and purified using a MinElute kit (Qiagen).