GSM7506819: d2_1_R1_ATACseq; Mus musculus; ATAC-seq
mESCs were collected at day2 and day4  and then washed two times in PBS, harvested, counted using a hemacytometer chamber and pelleted. 15.000 cells/sample for mESC were treated with Tagment DNA Buffer 2x reaction buffer with Tagment DNA Enzyme (Illumina) according to the manufacturer's protocol. After washes in PBS, cells were suspended in 50 mL of cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately spun down at 500 × g for 10 min at 4°C. Fresh nuclei were treated with Transposition mix and Purification (Illumina #FC121-130), the nuclei were incubated at 37°C in Transposition Reaction Mix (25 µL reaction buffer, 2.5 µL Transposase, 22.5 µL Nuclease free water), purified using Qiagen MinElute PCR Purification Kit (catalog no./ID: 28006) and eluted in 10 µL of nuclease free water. Sequencing library was prepared from the fragmented amplified tagmented DNA. Fragmentation size was evaluated using the Agilent 4200 TapeStation. Two biological replicates for each condition were sequenced using Illumina NextSeq500 system to obtain paired-end (PE) reads of 60 bp.