SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data.

ABSTRACT:

Background

Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-free RNA constitutes a background contamination that confounds the biological interpretation of single-cell transcriptomic data.

Results

We demonstrate that contamination from this "soup" of cell-free RNAs is ubiquitous, with experiment-specific variations in composition and magnitude. We present a method, SoupX, for quantifying the extent of the contamination and estimating "background-corrected" cell expression profiles that seamlessly integrate with existing downstream analysis tools. Applying this method to several datasets using multiple

SUBMITTER: Young MD 

PROVIDER: S-EPMC7763177 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature