Format

Send to

Choose Destination
Nat Methods. 2019 Aug;16(8):750-756. doi: 10.1038/s41592-019-0492-x. Epub 2019 Jul 29.

Gene expression atlas of a developing tissue by single cell expression correlation analysis.

Author information

1
German Cancer Research Center (DKFZ), Heidelberg, Germany.
2
Heidelberg University, Heidelberg, Germany.
3
CellNetworks-Cluster of Excellence, Heidelberg University, Heidelberg, Germany.
4
German Cancer Research Center (DKFZ), Heidelberg, Germany. m.boutros@dkfz.de.
5
Heidelberg University, Heidelberg, Germany. m.boutros@dkfz.de.
6
German Cancer Research Center (DKFZ), Heidelberg, Germany. a.teleman@dkfz.de.
7
Heidelberg University, Heidelberg, Germany. a.teleman@dkfz.de.

Abstract

The Drosophila wing disc has been a fundamental model system for the discovery of key signaling pathways and for our understanding of developmental processes. However, a complete map of gene expression in this tissue is lacking. To obtain a gene expression atlas in the wing disc, we employed single cell RNA sequencing (scRNA-seq) and developed a method for analyzing scRNA-seq data based on gene expression correlations rather than cell mapping. This enables us to compute expression maps for all detected genes in the wing disc and to discover 824 genes with spatially restricted expression patterns. This approach identifies clusters of genes with similar expression patterns and functional relevance. As proof of concept, we characterize the previously unstudied gene CG5151 and show that it regulates Wnt signaling. Our method will enable the leveraging of scRNA-seq data for generating expression atlases of undifferentiated tissues during development.

PMID:
31363221
PMCID:
PMC6675608
[Available on 2020-01-29]
DOI:
10.1038/s41592-019-0492-x

Supplemental Content

Full text links

Icon for Nature Publishing Group
Loading ...
Support Center