Power Analysis of Single Cell RNA-Sequencing Experiments

Single cell RNA sequencing (scRNA-seq) has become an established and powerful method to investigate transcriptomic cell-to-cell variation, revealing new cell types, and providing insights into developmental processes and transcriptional stochasticity. The array of published scRNA-seq protocols allow one to sequence transcriptomes from minute amounts of starting material. A key question is how these various protocols compare in terms of sensitivity of detection of mRNA molecules, and accuracy of quantification of expression. Here, we present an assessment of sensitivity and accuracy of many published data sets by spike-in standards with uniform data processing, including development of a flexible Unique Molecular Identifier (UMI) counting tool (https://github.com/vals/umis). We computationally compare 15 protocols, and experimentally assess 4 protocols on batch-matched cell populations, as well as investigating the impact of spike-in molecule degradation on two types of spike-ins. Our analysis provides an integrated framework for comparing different scRNA-seq protocols.