logoBrain Immune Atlas


The brain immune atlas provides a resource and visualization tool for assessing the single-cell RNA sequencing datasets generated by the Movahedi lab, which capture human and mouse brain immune cells in health and disease. You can visualize the expression of individual genes and/or download differentially expressed gene lists that define immune cell clusters. Gene-cell count and cell annotation matrices can be downloaded as well. Currently, our website hosts datasets originating from two publications: 1. Van Hove et al. Nature Neuroscience 2019; 2. Pombo-Antunes, Scheyltjens et al. 2020.


1. A single-cell atlas of mouse brain macrophages

2. Human and mouse Glioblastoma immune atlas

img overview index brain atlas
img overview index GBM

Using the 10x genomics chromium platform, we analyzed more than 61.000 CD45+ immune cells that were obtained from whole brains or isolated border regions, including the dura mater, subdural meninges and choroid plexus. Datasets were obtained from WT homeostatic mice, conditional Irf8 knockout animals and aged APP/PS1 transgenics.

Here, we mapped the glioblastoma immune landscape in newly diagnosed and recurrent patients and in mouse tumors via scRNA-seq and CITE-seq analysis. This revealed a large and diverse myeloid compartment, with dendritic cell and macrophage populations that were conserved across species and were dynamic across disease stages.



1. Hannah Van Hove, Liesbet Martens, Isabelle Scheyltjens, Karen De Vlaminck, Ana Rita Pombo Antunes, Sofie De Prijck, Niels Vandamme, Sebastiaan De Schepper, Gert Van Isterdael, Charlotte L. Scott, Jeroen Aerts, Geert Berx, Guy E. Boeckxstaens, Roosmarijn E. Vandenbroucke, Lars Vereecke, Diederik Moechars, Martin Guilliams, Jo A. Van Ginderachter, Yvan Saeys and Kiavash Movahedi. A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment. Nature Neuroscience 2019; 22:1021-35.

2. Ana Rita Pombo Antunes, Isabelle Scheyltjens, Francesca Lodi, Julie Messiaen, Asier Antoranz, Johnny Duerinck, Daliya Kancheva, Liesbet Martens, Karen De Vlaminck, Hannah Van Hove , Signe Schmidt Kjølner Hansen, Francesca Maria Bosisio, Koen Van der Borght, Steven De Vleeschouwer, Raf Sciot, Luc Bouwens, Michiel Verfaillie, Niels Vandamme, Roosmarijn E. Vandenbroucke, Olivier De Wever, Yvan Saeys, Martin Guilliams, Conny Gysemans, Bart Neyns, Frederik De Smet, Diether Lambrechts, Jo A. Van Ginderachter and Kiavash Movahedi. Single-cell profiling of myeloid cells in glioblastoma across species and disease stage reveals macrophage competition and specialization. Nature Neuroscience 2020.



The online tool is developed and maintained by Liesbet Martens (Saeys lab & Guilliams/Scott lab) and Daliya Kancheva (Movahedi lab). We hope you will find this resource useful and we would be happy to hear about your experiences and suggestions.

labFlask Kiavash Movahedi, PhD
Team Leader
Myeloid Cell Immunology Lab
VIB Inflammation Research Center (IRC)
Vrije Universiteit Brussel
Pleinlaan 2, 1050 Brussels, Belgium
Tel: +32-2-6291978
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