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Science. 2015 May 22;348(6237):910-4. doi: 10.1126/science.aab1601. Epub 2015 May 7.

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

Author information

1
University of Washington, Department of Genome Sciences, Seattle, WA, USA.
2
Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, OR, USA.
3
Illumina, Inc., Advanced Research Group, San Diego, CA, USA.
4
University of Washington, Department of Genome Sciences, Seattle, WA, USA. shendure@uw.edu.

Abstract

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.

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PMID:
25953818
PMCID:
PMC4836442
DOI:
10.1126/science.aab1601
[Indexed for MEDLINE]
Free PMC Article

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