Crafting a blueprint for single-cell RNA sequencing

Tom Denyer; Marja C P Timmermans

doi:10.1016/j.tplants.2021.08.016

Crafting a blueprint for single-cell RNA sequencing

Trends Plant Sci. 2022 Jan;27(1):92-103. doi: 10.1016/j.tplants.2021.08.016. Epub 2021 Sep 24.

Authors

Tom Denyer¹, Marja C P Timmermans²

Affiliations

¹ Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany.
² Center for Plant Molecular Biology, University of Tübingen, Auf der Morgenstelle 32, 72076 Tübingen, Germany. Electronic address: marja.timmermans@zmbp.uni-tuebingen.de.

PMID: 34580023
DOI: 10.1016/j.tplants.2021.08.016

Abstract

Droplet-based single-cell RNA sequencing (scRNA-Seq) has moved rapidly from a technology with great potential to a method applied to ever-broader questions. The detailed information that scRNA-Seq offers has proven incredibly powerful in resolving cell responses to developmental and environmental cues. However, to maximize the potential of this technology, a panoply of upstream, practical points require consideration. Principal among these are the optimization of cell-isolation procedures, accommodating biotic/abiotic stress responses, and discerning the number of cells and sequencing reads needed. To complement excellent reviews outlining applications and data analysis tools for scRNA-Seq, we here discuss these considerations and provide practical tips to tailor experimental design and ensure the best possible outcome.

Keywords: DropSeq; cell isolation; protoplasts; scRNA-Seq; single cell; transcriptomics.

Publication types

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

MeSH terms

Gene Expression Profiling
High-Throughput Nucleotide Sequencing
RNA* / genetics
Sequence Analysis, RNA
Single-Cell Analysis*

Substances

RNA