ATAC-seq is an assay that measures chromatin accessibility. In short, cells are treated with detergents to disrupt the cell and nuclear membranes, then treated with Tn5 transposase, which targets DNA that is accessible. Targeting includes cleaving the DNA and ligating DNA to the cut ends. DNA can be highly compacted and inaccessible, nucleosome free and very accessible, or in between. The Tn5 transpoase dimers are preloaded with Illumina adapters, so when two adapters are inserted into DNA close enough to one another and in the correct orientation the molecules can be PCR amplified and subjected to high-throughput sequencing. The ATAC-seq methods https://doi.org/10.1002%2F0471142727.mb2129s109 paper presents the figure below.