Scalable single-cell RNA sequencing from full transcripts with Smart-seq3xpress

Current single-cell RNA sequencing (scRNA-seq) methods with high cellular throughputs sacrifice full-transcript coverage and often sensitivity. Here we describe Smart-seq3xpress, which miniaturizes and streamlines the Smart-seq3 protocol to substantially reduce reagent use and increase cellular throughput. Smart-seq3xpress analysis of peripheral blood mononuclear cells resulted in a granular atlas complete with common and rare cell types. Compared with droplet-based single-cell RNA sequencing that sequences RNA ends, the additional full-transcript coverage revealed cell-type-associated isoform variation. Smart-seq3xpress enables single-cell RNA sequencing from full transcripts at high throughput.

Automated summary

Smart-seq3xpress is a simplified and miniaturized version of the Smart-seq3 protocol, which allows high-throughput single-cell RNA sequencing from full transcripts while reducing reagent usage. Analysis of peripheral blood mononuclear cells using Smart-seq3xpress revealed a comprehensive atlas of common and rare cell types. Compared with droplet-based methods, Smart-seq3xpress also provided additional coverage of cell-type-associated isoform variation.