ZEBRA - Brain Atlas

ZEBRA provides a comprehensive overview of single-cell and single-nucleus RNA sequencing data (scRNAseq/snRNAseq) in the context of neurodegenerative disease and brain aging. We include 10X Chromium samples from human as well as from mouse samples collected on GEO, Synapse, and the UCSC Cell Browser. We applied a unified preprocessing pipeline using quality control and normalization of the metadata. The datasets are integrated for each species individually. Missing cell type assignments are inferred based on a revised clustering and published marker genes.

Graphical abstract of the ZEBRA web server

This website is free and open to all users and there is no login requirement.

The Human cortex atlas comprises 1,930,270 cells and 21,158 genes across 19 data sets. In order to select the other datasets please click on the dropdown menu below the logo on the top left part of the website.

A tutorial with an overview of the web page is available in the Information section. The data sets are freely available under Downloads.

Please cite our manuscript under:

Flotho, M., Amand, J., Hirsch, P., Grandke, F., Wyss-Coray, T., Keller, A., and Kern, F. "ZEBRA: A Hierarchically Integrated Gene Expression Atlas of the Murine and Human Brain at Single-Cell Resolution." Nucleic Acids Research, November 6, 2023, gkad990. https://doi.org/10.1093/nar/gkad990.