ATAC-Seq Library Preparation Protocol

The ATAC-Seq experiments were performed as described previously^{37 (link)}. We performed two biological replicates per condition. Briefly, 50,000 cells were used per reaction. Nuclei were isolated after resuspension and centrifugation in Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 1% (v/v) Igepal CA-630). The 50 µl transposase reaction with isolated nuclei (plus 25 µl TD, 2.5 µl TDE1 and 22.5 µl H₂O) was incubated at 37 °C for 30 min. DNA was purified using a MinElutePCR purification column (Qiagen). The transposed DNA fragments were preamplified by a first PCR reaction with five cycles containing barcoded Nextera PCR primers. The optimal number of cycles was determined by a SybrGreen qPCR reaction containing a 5-µl aliquot from the first PCR. The second PCR was then carried out with eight cycles and the libraries were first purified by MinElutePCR purification column (Qiagen) and then further size-selected by AMPure XP beads to obtain libraries with a size distribution between 150 and 1000 base pairs.