Stably expressed genes in single-cell RNA sequencing

摘要

Motivation: In single-cell RNA-sequencing (scRNA-seq) experiments, RNA transcripts are extracted and measured from isolated cells to understand gene expression at the cellular level. Measurements from this technology are affected by many technical artifacts, including batch effects. In analogous bulk gene expression experiments, external references, e.g. synthetic gene spike-ins often from the External RNA Controls Consortium (ERCC), may be incorporated to the experimental protocol for use in adjusting measurements for technical artifacts. In scRNA-seq experiments, the use of external spike-ins is controversial due to dissimilarities with endogenous genes and uncertainty about sufficient precision of their introduction. Instead, endogenous genes with highly stable expression could be used as references within scRNA-seq to help normalize the data. First, however, a specific notion of stable expression at the single-cell level needs to be formulated; genes could be stable in absolute expression, in proportion to cell volume, or in proportion to total gene expression. Different types of stable genes will be useful for different normalizations and will need different methods for discovery.