Abstract
Housekeeping genes are critical for understanding the core transcriptome and instrumental in data normalisation given their stable expression in different tissues and cells. Previous studies defined housekeeping genes using bulk transcriptome data. With recent advances in single-cell RNA-sequencing (scRNA-seq), it is now possible to identify steadily expressed genes across individual cells. Here we introduce the concept of housekeeping index and a framework for assessing housekeeping genes at the single-cell level using high-resolution scRNA-seq data. We apply our approach on two scRNA-seq datasets from early mammalian development and evaluate derived housekeeping genes on ten additional scRNA-seq datasets from diverse cell/tissue types.
Copyright
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