Single Cell Analytics

Single Cell Analytics

Learn the basics.

A 5 minutes tutorial on single cell analytics.

New to the field? No background in biology or analytics? Find out how single cell genomics may impact your life and why we are working in this research domain.

What is Single Cell Sequencing?

All organisms (including humans) are built from cells. Those cells contain complicated molecules, called DNA and RNA. Think of DNA as a blueprint, think of RNA as the stuff built from that blueprint. In your cells, DNA is transcribed into RNA, and RNA is translated into proteins, which determine the functions your cell is performing. With transcriptomics, we study the RNA in cells to understand their functions better.

For many years now, researchers are able to read the content of cells, be it RNA or DNA. For this, they had to mix many cells together to get enough material for the sequencing machines, this way blurring the signal from individual cells. Only recently have we been able to sequence each cell individually – now we can study life at its most basic unit!

What is new about single cell sequencing?

In genome research, researchers often perform case-control-studies: they sequence RNA from patients of a disease and a healthy control group, and search for differences in the genomic measurements.

To understand the difference between single cell sequencing and normal (“bulk”) sequencing, think of comparing two smoothies: they might look the same, even taste the same, but one of them might be poisonous and you will never know the difference, because the recipe is hidden once everything is mixed together. In the same way, researchers may miss biological signals when they mix together cells in in bulk sequencing.

What can you learn from a single cell?

  • Cell Type Discovery

    With single cell sequencing, we can now better understand the different types of cells that perform different functions within an organism, and identify new types.

  • Population Decomposition

    Cells are working together within a tissue, they are communicating and influencing each other. With single cell sequencing, we can now study the different cell types within a tissue, their reletive abundances and how they interact with each other.

  • Rare Cell Identification

    Some diseases might be governed by the presence or absence of rare cells. With single cell sequencing, you can finally identify them in the mix of cells that are found in a tissue sample.

  • Subtype Classification

    For many cell types, researches thought that all cells of that type are the same, basically because they looked the same under a microscope. It turned out that cells of the same type can behave very differently, and we are now learning more about different sub-cell-types and their characteristics.

  • Cell Dynamics

    Cells change over time – they perform functions, they make use of nutrients, they grow old. With single cell sequencing, we can now study those processes much better.

What can you do with the results?


The human immune system consists of a wide range of different cell types, helping each other in complex ways. Disturbances in the system cause a wide range of inflammatory diseases such as rheumatic arthritis, chronic bronchitis or certain inflammatory gut diseases. By improving our understanding of the cell types, maybe even extending the list of known types, and by studying their interactions, we may find cures to those diseases.


Neurons, the cells of our brain, are very versatile, and we don’t know much about them and how they influence each other. So far, researchers mostly studied neurons under the microscope, distinguishing them by shape. Now we are able to study neurons separately and get a much better understanding of their interactions. This will improve our understanding of a range of neural diseases.