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

Darren A. Cusanovich, Riza Daza, Andrew Adey, Hannah A. Pliner, Lena Christiansen, Kevin L. Gunderson, Frank J. Steemers, Cole Trapnell, Jay Shendure

Research output: Contribution to journalArticlepeer-review

714 Scopus citations


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 coordinately regulated chromatin accessibility at the level of single cells both between and within cell types, with a scalable method that may accelerate progress toward a human cell atlas.

Original languageEnglish (US)
Pages (from-to)910-914
Number of pages5
Issue number6237
StatePublished - May 22 2015

ASJC Scopus subject areas

  • General


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