Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

Technical advances have enabled the collection of genome and transcriptome data sets with single-cell resolution. However, single-cell characterization of the epigenome has remained challenging. Furthermore, because cells must be physically separated before biochemical processing, conventional single-cell preparatory methods scale linearly. We applied combinatorial cellular indexing to measure chromatin accessibility in thousands of single cells per assay, circumventing the need for compartmentalization of individual cells. We report chromatin accessibility profiles from more than 15,000 single cells and use these data to cluster cells on the basis of chromatin accessibility landscapes. We identify modules of…

• PG
  Paul G. Allen Family Foundation
• DR
  Damon Runyon Cancer Research Foundation

  Award: DFS-#10-14
• NI
  National Institutes of Health

  Award: 1DP1HG007811