ATAC-seq: Profiling Chromatin Accessibility

ATAC-seq analysis was performed as recently described (56 (link)). Briefly, 5×10⁴ cells for each condition were first incubated in hypotonic buffer then resuspended in lysis buffer, centrifugated and resuspended in Transposase reaction mix for additional 30 min at 37C, following manufacturer recommendations (Nextera DNA sample Prep Kit, Illumina). After DNA purification, adaptor sequences were added to the fragmented DNA by PCR. Purified PCR products were sequenced using the Illumina Nextseq device. Paired end reads were aligned to hg19 using BWA (48 (link)). Read start sites were adjusted to represent the center of the transposon binding event (+4 bp in the plus strand and −5 bp in the minus strand). Signal densities were calculated over a sliding 150 bp window at 20 bp steps and normalized to 10M reads in each experiment.