Glomerulus single-cell gene expression atlas

A Single-cell Transcriptome Atlas of the Mouse Glomerulus

Nikos Karaiskos1*, Mahdieh Rahmatollahi2*, Anastasiya Boltengagen1, Haiyue Liu1, Martin Hoehne2, Markus Rinschen2,3, Bernhard Schermer2,4,5, Thomas Benzing2,4,5, Nikolaus Rajewsky1, Christine Kocks1#, Martin Kann2*, Roman-Ulrich Müller2,4,5*#

1 Systems Biology of Gene Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany.
2 Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
3 Scripps Institute, San Diego, CA, USA
4 Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany.
5 Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany.

* These authors contributed equally to this work.
# To whom correspondence should be addressed:, and

The glomerulus single-cell atlas is created and maintained by Nikos Karaiskos.


The following features are currently supported in the atlas:

  • Clustering offers an overview of the single-cell RNA sequencing data and 2D tSNE representation of the major cell types. Clustering can be queried for the expression of a given gene. Gene symbols are required.
  • The clustering is supported from violin plots, showing expression of the selected genes along the major cell types.
  • The "Endothelium" and "Podocytes" tabs show the subclustering of the corresponding cell types. The format is the same as described above.

Data availability

The raw (fastq files), as well as processed data (digital gene expression matrices for each replicate) is available at the GEO database under the accsession number GSE111107.

The final normalized, filtered gene expression matrices (after removing low quality cells and doublets) with cluster information can be downloaded directly for the full set of cells, the endothelial cells, or the podocytes.

Genome tracks

Genome tracks for the major cell types from the pooled replicates are available here.

Release notes

  • 20 August 2018: the normalized, filtered gene expression matrices with cluster information were made available for download.
  • 21 March 2018: added features of the atlas, data availability and genome tracks.
  • 27 February 2018: database goes online.