News Release 

New method to purify cell types to high purity

Cell type purification by single-cell transcriptome-trained sorting

Hubrecht Institute


IMAGE: The desired cells, in this case blood stem cells (dark blue) are strongly enriched in the cell population with GateID. The first bar graph shows the composition of the cell... view more 

Credit: Chloé Baron, Mauro Muraro and Aditya Barve, © Hubrecht Institute.

Researchers from the group of Alexander van Oudenaarden at the Hubrecht Institute (KNAW) have developed GateID, a new method that can highly purify a cell type of interest from a tissue, without the use of antibodies or a genetic reporter. Thereby, GateID allows to isolate a variety of cell types, such as stem cells, in order to study them in more detail. The researchers have published their results in the scientific journal Cell on the 3rd of October.

Specific cell types

Our bodies are made up of millions of cells, among which are many different cell types and subtypes carrying out different tasks in the body. For example, stem cells are a rare subtype of cells crucial for organ formation and maintenance. Additionally, tumors consist of different cell types, each one potentially responding differently to treatment. Overall, studying individual cell types and subtypes is important to obtain a better understanding of their properties and function in health and disease.


Until now, single cells that belong to a certain cell type of interest, such as stem cells, are purified based on specific markers present on the outside of the cell. For the purification, researchers use fluorescent antibodies able to bind these markers or generate genetically modified organisms where the cells of interest are fluorescently labelled. In both cases, the fluorescent cells can be detected and specifically purified by a flow cytometer. While powerful, these approaches are not always available. For example, genetic modifications are impossible in humans and antibody availability are not always available. Therefore, certain cell types remain inaccessible to researchers due to the lack of purification solutions.

New tool

Researchers at the Hubrecht Institute have developed a new tool, called GateID, that enables the purification of cell types purely based on the native characteritics of the cells. GateID uses characteristics such as shape, size and granularity that can be measured by a flow cytometer, the same equipment used for cell type purification based on the above-mentioned antibodies and genetic markers. This new approach makes it possible to purify a cell type of choice without having to resort to genetically modified organisms or commercially available antibodies.


GateID uses two types of information: information from inside and outside the cell. First, researchers generate a dataset by collecting single cells from the organ or tissue of choice. For each single cell, both the native characteristics of the cells (how they look from the outside) and their specific gene expression profiles (how they look on the inside) are measured. The researchers then identify the cell type of each single cell through their gene expression profiles. The native characteristics are then coupled to the identified cell type. Next, GateID is able to select the best native characteristics to purify the desired cell type in many subsequent experiments. The researchers show that GateID allows for the isolation of several cell types to high purities.

Purifying blood and pancreatic cell types

In their study, the researchers used GateID to purify four cell types from the zebrafish immune system, including blood stem cells and progenitor cells, and alpha and beta cells from the human pancreas. In the future, researchers will be able to use GateID to purify and study any cell type of choice, from stem cells to tumor cells.


Alexander van Oudenaarden is director of the Hubrecht Institute, group leader, professor of Quantitative Biology of Gene Regulation at the UMC Utrecht and Utrecht University and Oncode Investigator.

About the Hubrecht Institute

The Hubrecht Institute is a research institute focused on developmental and stem cell biology. It encompasses 22 research groups that perform fundamental and multidisciplinary research, both in healthy systems and disease models. The Hubrecht Institute is a research institute of the Royal Netherlands Academy of Arts and Sciences (KNAW), situated on Utrecht Science Park. Since 2008, the institute is affiliated with the UMC Utrecht, advancing the translation of research to the clinic. The Hubrecht Institute has a partnership with the European Molecular Biology Laboratory (EMBL). For more information, visit

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