A single cell plate-based three-level combinatorial indexing assay that measures chromatin accessibility. The first two rounds of split-pool indexing are achieved by successive ligations to each end of the Tn5 transposase complex, and the third round remains through PCR. The protocol no longer requires cell sorting and has been optimized to maximize recovery of fragments per cell. [ http://www.ncbi.nlm.nih.gov/pubmed/33184180 https://orcid.org/0000-0003-4389-9821 ]