Skip to main content
eScholarship
Open Access Publications from the University of California

UCSF

UC San Francisco Previously Published Works bannerUCSF

CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues.

  • Author(s): Przytycki, Pawel F
  • Pollard, Katherine S
  • et al.

Published Web Location

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02279-1
No data is associated with this publication.
Abstract

Single-cell and bulk genomics assays have complementary strengths and weaknesses, and alone neither strategy can fully capture regulatory elements across the diversity of cells in complex tissues. We present CellWalker, a method that integrates single-cell open chromatin (scATAC-seq) data with gene expression (RNA-seq) and other data types using a network model that simultaneously improves cell labeling in noisy scATAC-seq and annotates cell type-specific regulatory elements in bulk data. We demonstrate CellWalker's robustness to sparse annotations and noise using simulations and combined RNA-seq and ATAC-seq in individual cells. We then apply CellWalker to the developing brain. We identify cells transitioning between transcriptional states, resolve regulatory elements to cell types, and observe that autism and other neurological traits can be mapped to specific cell types through their regulatory elements.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Item not freely available? Link broken?
Report a problem accessing this item