The CeNGEN project

Single-cell data released

The second data release is described in an updated preprint, and can be explored at the updated Web App.

We completed single cell RNA-Sequencing of every neuron class in C. elegans. We provide a web app at cengen.shinyapps.io/CengenApp for interactive exploration of the dataset. Detailed methods and in-depth analyses of the dataset are described in a preprint that can be accessed at biorxiv.org/content/10.1101/2020.12.15.422897v1. The FASTQ files have been deposited at GEO under accession number GSE136049.


Differential gene expression defines individual neuron types and determines how each contributes to circuit physiology and responds to injury and disease. The C. elegans Neuronal Gene Expression Map & Network (CeNGEN) will establish a comprehensive gene expression atlas of an entire nervous system at single-neuron resolution.

Two approaches are being used:

1) single-cell RNA-Sequencing, which allows the identification of each neuronal class;

2) deep bulk RNA sequencing of sorted neurons from each class enables full characterization of its transcriptome and of non-coding RNAs.

You can find a full description in Hammarlund, Marc et al., Neuron, Volume 99, Issue 3 430-433, doi:10.1016/j.neuron.2018.07.042

This project was made possible by the support of the NIH NINDS (grant R01NS100547) and the C. elegans research community.