Anthropology and Human Genetics

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scRNA-seq assay overview

Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data from 583 mouse embryonic stem cells to evaluate six prominent scRNA-seq methods: CEL-seq2, Drop-seq, MARS-seq, SCRB-seq, Smart-seq, and Smart-seq2.

While Smart-seq2 detected the most genes per cell and across cells, CEL-seq2, Drop-seq, MARS-seq, and SCRB-seq quantified mRNA levels with less amplification noise due to the use of unique molecular identifiers (UMIs). Power simulations at different sequencing depths showed that Drop-seq is more cost-efficient for transcriptome quantification of large numbers of cells, while MARS-seq, SCRB-seq, and Smart-seq2 are more efficient when analyzing fewer cells.

Our quantitative comparison offers the basis for an informed choice among six prominent scRNA-seq methods, and it provides a framework for benchmarking further improvements of scRNA-seq protocols.

For more information on scRNA-seq benchmarking, refer to Ziegenhain et al. (2017).

     Drop-Seq SCRB-seq Smart-seq/C1
single-cell isolation Droplet FACS Microfluidics
ERCC spike-ins Χ
Full-length coverage Χ Χ
Protocol exists for bulk Χ
Imaging of cells possible Χ Χ
Sequencing PE PE SE