ATAC-Seq Protocol with Modifications

The ATAC-Seq was performed by Active Motif as described by Buenrostro et al. [32 (link)], with some modifications based on Corces et al. [52 (link)]. Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina, Inc.). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified. The ATAC-Seq libraries were sequenced as 45 bp paired-end libraries on a NextSeq 500 and mapped to the human (version hg19) or mouse (version mm10) genomes using BWA [53 (link)] with default parameters. Reads were filtered using Illumina’s sequence quality filters, and PCR duplicates were removed. Peaks were called using MACS1.4.2 at a cutoff of p-value = 1e-7, without control file, and with the–nomodel option [54 (link)]. Peaks were merged for all samples of the same background, reads were counted for each region, and differential analysis was performed between each modified sample and its parent strain using DESeq2 [37 (link)].