How deep is enough in single-cell RNA-seq?

Guidelines for determining sequencing depth facilitate transcriptome profiling of single cells in heterogeneous populations.

In recent years, single-cell RNA-seq has emerged as a powerful, new approach for characterizing the cell types present in a mixed population. These studies usually involve a trade-off between the number of samples analyzed and the number of RNA transcripts sequenced per cell, or sequencing depth, that can be achieved. In the current issue of Nature Biotechnology, Pollen et al. present quantitative guidelines for determining the sequencing depth necessary to distinguish the cell types in a complex sample. Using a commercial microfluidic platform to capture hundreds of cells from a variety of human tissues and performing RNA-seq to different depths, they demonstrate accurate and reliable classification of cell types at a sequencing depth of only 50,000 reads per cell about two orders of magnitude fewer than what has been typically reported.


Pollen AA et al. (2014) Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nat Biotechnol 32(10):1053-1058. [abstract]


Streets AM, Huang Y. (2014) How deep is enough in single-cell RNA-seq? Nat Biotechnol 32(10):1005-1006. [abstract]