Applications of single-cell sequencing

Single-cell sequencing is used in various fields of research. This page provides an overview of the different solutions we provide with our services for our customers.

Cell type identification


When pooling many cells for sequencing analysis, the information derived from the sample is always the average of all the cells in the starting material. This means that the most abundant cell types will dominate the results. With single-cell sequencing, every cell is analyzed individually. The result is that each cell from the starting material will have its own unique profile, which allows the researcher to identify the different cell types that are present in the sample.

Target Discovery


Different cell types have different repertoires of cell surface markers. These molecules, apart from performing their biological function, are used to specifically capture different cell types by labeling them with (fluorescent) antibodies. These surface marker repertoires of different cell types are of great interest for pharmaceutical companies because they are potential targets for new pharmaceutical substances.



An important, and relatively recent, realization in the oncology field is that a tumor is usually far from a homogeneous collection of cells. In fact, tumors usually consist of different cell types that can play different roles in its development or resistance to therapy. Besides cancer cells, a tumor also has a micro environment containing blood vessels, immune cells and other native cell types. Tumor heterogeneity and the tumor micro environment can be investigated by sequencing the cells from a tumor individually, to better understand the relationship between all the different cell types. Understanding how heterogeneous cancer really is, can be vital for personalized therapy decisions for the patient.

Developmental biology


In the field of developmental biology, one of the most important research subjects is the differentiation of stem cells to specialized cell types. The difficulty with stem cells is that they are rare and often not actively dividing. This means that they are difficult to analyze, especially with bulk sequencing methodologies. Single-cell sequencing offers an excellent opportunity to specifically select stem cells for further genetic analysis and to trace their differentiation pathways, increasing the understanding of their development.

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