title: Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
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.
authors.affiliation: University of Washington, Department of Genome Sciences, Seattle, WA, USA.
authors.forename: Darren A
authors.initials: DA
authors.lastname: Cusanovich
authors.affiliation: University of Washington, Department of Genome Sciences, Seattle, WA, USA.
authors.forename: Riza
authors.initials: R
authors.lastname: Daza
authors.affiliation: Oregon Health and Science University, Department of Molecular and Medical Genetics, Portland, OR, USA.
authors.forename: Andrew
authors.initials: A
authors.lastname: Adey
authors.affiliation: University of Washington, Department of Genome Sciences, Seattle, WA, USA.
authors.forename: Hannah A
authors.initials: HA
authors.lastname: Pliner
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, CA, USA.
authors.forename: Lena
authors.initials: L
authors.lastname: Christiansen
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, CA, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.affiliation: Illumina, Inc., Advanced Research Group, San Diego, CA, USA.
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Steemers
authors.affiliation: University of Washington, Department of Genome Sciences, Seattle, WA, USA.
authors.forename: Cole
authors.initials: C
authors.lastname: Trapnell
authors.affiliation: University of Washington, Department of Genome Sciences, Seattle, WA, USA. shendure@uw.edu.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
mesh_terms: D002843:Chromatin / Q000378:metabolism*; D044127:Epigenesis, Genetic; D057809:HEK293 Cells; D018922:HL-60 Cells; D006801:Humans; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D002843:Chromatin