Scalable single-cell profiling of chromatin modifications with sciCUT&Tag

Cleavage Under Targets & Tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing precipitation-based methods. The efficiency of the method enabled chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution high-throughput single-cell chromatin profiling. We describe a pipeline for single-cell indexed CUT&Tag (sciCUT&Tag) that uses SNPs to facilitate doublet-cell removal and minimize batch effects. We illustrate the optimized protocol by analysis of mouse and human cell lines, as well as human peripheral blood mononuclear cells. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells. Overall design: We used Cleavage under targets and Tagmentation (Cut-and-Tag), a chromatin profiling strategy in which antibody-targeted controlled integration of DNA sequencing adapters produces libraries for paired-end DNA sequencing.