Three reasons to start small with single-cell sequencing

When you first start with single-cell sequencing or with a new project, it’s often best to start small. We call this a pilot project. Here, we explain why.

Technical validation 

If you start a new single-cell sequencing project, you need to validate if you’re using the right protocols in your own lab and if you have chosen the correct parameters. 

Whether you send us a single cell suspension or cells sorted in plates, it is important to figure out if your samples are of good quality. 


There are several things that can happen when something in your protocol is not optimal. If the viability of your sample is low – we use <70% as a benchmark- you will have less viable cells in your data than you might have expected. This means fewer cells to include in your analysis.  

Or, you might end up with clusters based on your samples: a batch effect. In that case, you need to correct this effect in your data, hoping you can still draw conclusions. 

To avoid this, we recommend a small pilot project to make sure that your protocol is fully optimized, and you are ready for that big singlecell project. 

Furthermore, starting small allows you to optimize your project design. If you collect single-cell data from a few samples, you can use that data tadjust your original plan. 

For example, you might need to sequence deeper to be able to identify all cell types. Or, you have more than enough cells in your dataset, which allows you to lower the number of cells per sample.  

Based on your pilot project data, we can decide together how to proceed. If you want to learn more about project design, visit our blog “how to decide your single-cell sequencing parameters”.

Biological validation 

A single-cell sequencing pilot project allows you to analyze a small data set to draw validate if the project will yield interesting results. This is especially recommended if you are not sure about the outcome. For example, when you are interested in comparing two patient groups, or samples before and after treatment 

A pilot project is perfect to indicate if you can expect a valuable outcome. 

Fewer risks 

Since single-cell sequencing is expensive, it is a risk to start with a large single-cell sequencing project without technical or biological validations.  

A pilot project can assure you whether or how you should proceed and spend all that money – or not.  


Interested in a pilot project? You can book a meeting with one of our specialists here. 

Other articles