The last decade has seen a revolution in high-throughput single-cell analysis, where gene expression and other cellular states can be measured from small sample quantities. This accelerated development has improved the accessibility and affordability of the technology, transforming capabilities in basic and clinical research.
Sample preparation for single-cell analysis is just as important as the downstream analysis, as poor sample quality will yield inaccurate or incomplete results.
Download this guide to explore tips on:
- Sample selection and experimental planning
- Cell handling, cell isolation and quality control measures
- Working with complex samples
How To Guide
Sample Prep Tips for Single-Cell Analysis
Kaja Ritzau-Reid, PhD
Single-cell analysis allows individual cells to be studied, capturing cell-to-cell variability in a specifi
biological niche (such as an organ or tissue).1 The last decade has seen a revolution in high-through
put
single-cell analysis, where gene expression and other cellular states can be measured from small
sample quantities.2 This accelerated development has made the technology more accessible and
affordable to researchers and clinicians, transforming capabilities in basic and clinical research
.2–4
Cellular variability can be captured at different levels, from the genome, transcriptome, epigenome,
proteome and metabolome. Jointly, these are commonly referred to as “multiomics”. In recent years,
multiomics technologies have been developed to measure multiple layers of cellular heterogeneity at
the same time.
5,6
Sample preparation for single-cell analysis is just as important as the downstream analysis, as poor
sample quality will yield inaccurate or incomplete results. This guide will provide tips and tricks to
prepare a high-quality single-cell suspension that is broadly applicable to most cell and tissue types.
The first part of this guide will cover the initial stages of sample selection and general best practice in
experimental planning and organization. The second part will cover practical cell handling tips, quality
control measures, cell isolation best practices and tips for working with complex samples.
Work cleanly, work quickly
While it may sound obvious, careful experimental planning and organization are key to achieving good
results. This is particularly true for single-cell preparation protocols that require you to work quick
ly
and efficiently to reduce the risk of sample degradation, downstream transcriptional changes or
sample contamination. Simple steps such as keeping an organized and clean workbench are essential
for this. Start as you plan to go on: use clean personal protective equipment (PPE), regularly clean your
workbench so that it is free of DNA or RNA contamination, change gloves regularly and ensure that
your hood has effective airflow and HEPA filtration to protect your sample and, if necessary, you. Use
cold temperatures to minimize sample degradation and work quickly to reduce cell handling time.
Choose your sample
Clearly defining your experimental goals will help to determine the best sample input and preparation
technique. It’s important to consider the potential complexities of your selected sample: if you are using
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