Single-cell sequencing: Common applications

Single-cell sequencing: Common applications

Single-cell RNA sequencing can be used for almost every biological question that requires a detailed understanding of a cell population. So, it’s hardly surprising that it has so many different applications.

This post is a brief overview of just some of the areas where researchers utilize single-cell RNA sequencing.


Identify cell types

Biological samples are rarely homogenous and can contain multiple cell types – this is true whether you work with primary tissue, clinical samples such as tumor biopsies, a cell line, or organoids.

Single-cell RNA sequencing allows you to identify exactly which cell types (and subtypes) are present in your sample, as well as the ratio between them.

If you study sample heterogeneity at a single-cell level, you may even identify cell types you were not expecting. And if you’re very lucky, you’ll discover completely new cell types (or sub-types) in your tissue that have not been described before.

Read more on our cell type identification page.


Discover and develop new drug targets

Proteins inside cells and on cell surfaces can be excellent drug targets. Single-cell sequencing is a powerful tool to identify these targets, combining knowledge of disease-specific cellular pathways with single-cell transcriptomics.

Once you can identify a target and test specific drugs, single-cell sequencing will help you to assess drug efficiency on your target pathway and cell type.

Therefore, single-cell RNA sequencing can help you select your most promising drugs: those that only target your cell type and protein of interest, and verify whether or not it works as expected.

Read more on our drug discovery page.


Reconstruct cell development pathways

Cells can change over time in many ways. Some may differentiate stem cells into mature cells, while others react to changes in their environment. Moreover, administering drugs can activate some immune cells.

Single-cell sequencing allows you to study these changes in greater detail by comparing different time points. You can then use this data to place all single cells along a pseudotemporal trajectory, for example from the most stem cell-like cell to the cell in the last differentiation stage.

You can also use it to analyze how cells change in response to adding a growth stimulus, study patient samples before and after treatment, or assess the response of immune cells to cancer cells. The possibilities are endless.


Single-cell Biodistribution

One of the most promising novel therapy modalities is in vivo gene therapy. Here, vectors like adeno-associated viral vectors deliver healthy genes and/or gene editing machinery to diseased cells.

Optimizing the specificity of such vectors is a key aspect of this technology’s development. With its ability to detect transgenes at single-cell resolution, single-cell sequencing is a suitable technology to fuel this exciting development.

Read more on our biodistribution page


Immune profiling

The specificity of immune cells varies considerably and depends on the recombination of variable regions in the genome. With millions of possible combinations, the ability to study the immune repertoire at the single-cell level opens up tremendous possibilities for researchers.

Single-cell sequencing, combined with single-cell immune profiling, allows you to determine the complete repertoire of your immune cells, including full-length immunoglobin sequences, isotypes, and T-cell receptors.

If you then combine your single-cell immune repertoire information with single-cell transcriptomics, you can discover new immune cell types and states.

Your can then use your immune profiling data to create immune cell atlases, characterize immune responses, or identify immune cells within the tissue microenvironment.

Read more on our immune profiling page


And more

Single-cell sequencing can be used to answer many scientific questions. As we said before, the possibilities are endless!

If you’re wondering whether – or how – to apply single-cell sequencing in your field, we can help.

Supercharge your mind with all the single-cell sequencing fundamentals by downloading our ultimate guide.