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

Michael Hagemann-Jensen; Christoph Ziegenhain; Rickard Sandberg

doi:10.1038/s41587-022-01311-4

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

Nat Biotechnol. 2022 Oct;40(10):1452-1457. doi: 10.1038/s41587-022-01311-4. Epub 2022 May 30.

Authors

Michael Hagemann-Jensen^#¹, Christoph Ziegenhain^#¹, Rickard Sandberg²

Affiliations

¹ Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden.
² Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden. rickard.sandberg@ki.se.

^# Contributed equally.

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling / methods
High-Throughput Nucleotide Sequencing / methods
Leukocytes, Mononuclear* / chemistry
Protein Isoforms
RNA / analysis
RNA / genetics
Sequence Analysis, RNA / methods
Single-Cell Analysis* / methods

Substances

Protein Isoforms
RNA