The CeNGEN project

Alternative splicing tools

New tool available: you can now look at alternative splicing in many neuron types of the worm brain! Access it at

In the initial phase of the CeNGEN project, we generated gene expression profiles of every neuron type in the worm brain. However, because of its 3′ bias, this data doesn’t tell you which specific isoform is expressed in each neuron. Thus, we have also been generating bulk RNA-Seq profiles of individually sorted neuron types. We could obtain a uniform coverage along the gene bodies by using the rRNA depletion method described here, which makes this data ideal to study splicing! While we are still actively sequencing, we recently released a first set covering 41 neuron types, described in this preprint which also develops ways to integrate this new bulk data with our previous scRNA-Seq and takes a look at ncRNAs.

As splicing is a complex phenomenon, we are releasing 3 complementary tools to look at the data from different angles. The transcript-level quantification is easy to interpret in simple genes and gives a good overview, but is more sensitive to noise and less accurate. The event-level quantification, while harder to interpret, allows you to find interesting events across all neurons. The genome browser view gives direct access to the raw data and can help contextualize the results of the other tools.

Please note that this data and tools are a work in progress, we are developing various ways to improve cleaning and validation. Feel free to contact us for questions or suggestions!

Updates to the single-cell app

We made some updates to the single-cell web app. It is available at the previous URL. The old App is still running at Changes:

  • improved performance
  • removed single cell plot
  • for differential testing, removed all tests other than Wilcoxon, implemented pseudobulk testing methods. See the updated documentation.

Single-cell paper published

Our results from single-cell RNA-Seq are officially out in Cell (DOI: 10.1016/j.cell.2021.06.023). The data can be explored online with the updated CeNGEN app. See here for details.

International Worm Meeting 2021

During our workshop at the IWM 2021, we performed live demonstrations of the web app.

Other presentations:

  • Erdem Varol, A computational approach linking neuron-specific gene expression with connectivity, Talk 20Synaptic Function and Circuits, June 21
  • Lidia Ripoll-S├ínchez, Mapping the neuropeptidergic connectome of Caenorhabditis elegans, Talk 22 Synaptic Function and Circuits, June 21
  • Alec Barrett, Integrating bulk and single cell transcriptomics for accurate detection of tissue-specific gene expression, Poster 568A, June 21st
  • Seth Taylor, Molecular topography of an entire nervous system, Poster 837C, June 23rd

Single-cell data released

See the corresponding page for details on how to explore the dataset. See our preprint for the full set of analyses.

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) is working to 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.