Single-cell sequencing: Research areas

Single-cell sequencing: Research areas

Because of its wide range of applications, single-cell sequencing is applied in many different research fields. This post is a brief overview of some of the areas where single-cell RNA sequencing is advancing research.


A tumor is never a homogenous mass of cells – it’s a mixture of different tumor cell types, each of which influences the tumor in a different way.

Non-tumor cell types such as blood vessels or immune cells also influence the proliferation and survival of the cancer. This makes it difficult to pinpoint the molecular mechanisms at work precisely when analyzed using average bulk RNA seq expression data.

The highly increased resolution of single-cell sequencing allows you to assess the heterogeneity of your tumor samples and understand how they behave in their microenvironment.

For example, identifying subpopulations of tumor and non-tumor cells may lead to better insight into the molecular mechanisms behind processes such as metastasis or therapy resistance.



Developmental Biology

As they develop, stem cells follow a differentiation pathway, where they differentiate into progenitor and mature cells. In some species, these developmental processes can be reactivated in order to regenerate tissue.

Understanding the underlying molecular processes has important implications for both congenital diseases and regenerative medicine.

Single-cell sequencing allows you to study the developmental models of your interest at the level of individual stem or progenitor cells and determine cell lineage. You can identify differentiation stages and corresponding cell types from stem cell to mature cell, in any species and any cell type.

You can then use this data to create lineage trees with a pseudo temporal analysis, or use your transcriptomics data to identify molecular mechanisms in your cell that drive development or regeneration.

Read more on our developmental biology page



The immune system is very complex, with many different cell types (and sub-types) and immune responses. Studying this field at high resolution with single-cell sequencing can increase our understanding of these complex processes.

You can use single-cell sequencing to identify and characterize immune cell types in your sample, including their cell surface markers. It’s also possible to identify antigen specificity for further characterization of immune cell population or antibody discovery.

And you can discover the molecular drivers and potential new cell subtypes behind immune responses with single-cell transcriptomics data.

Read more on our immunology page.



Neuroscience is another complex field that benefits from increased resolution data obtained using single-cell sequencing. The central nervous system is a complex structure with many different cell types and signaling pathways.

You can gain more insight into molecular mechanisms of neural function, disease, and injury by comparing different states with single-cell gene expression.

You can also use single-cell sequencing to identify known or rare cell populations or search for novel biomarkers to target in specific diseases, or to study brain development in detail.

Read more on our neuroscience page.


And more

Of course, single-cell sequencing is not limited to these research areas. 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.

Get the ultimate guide to supercharge your mind with all single-cell sequencing knowledge basics.