This website aims to be a handy collection of all publicly available C. elegans single cell and single nucleus RNA sequencing data. In addition to listing studies and the original data sources, for convenience the data has been repackaged and a direct download link to the data in .h5ad format is provided. The GitHub repository of this website is https://github.com/munfred/wormcells-data, and the .h5ad files are hosted on the repository’s releases page.

The .h5ad files provided here with the annotations from different studies the here can be readily used to perform differential expression between cell types of interest using a tutorial notebook written to be run on Google Colab. Click the button below to open a notebook and run it.

Open In Colab

It loads an example C. elegans dataset with 100k cells and 169 cell types with data from the data from the CeNGEN project published by Taylor et al 2020, and spins up a simple app for using a table like interface for performing differential expression. The code for the app is available at https://github.com/munfred/scdefg

Short Name Total cells Method h5ad Summary Article/preprint Original Data Notes
Cao 2017 35,987 sci-RNA-seq 136MB L2 larvae A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution Science 2019. GSE98561 and GSM4318946 (reprocessed) GSM4318946 release was a reannotation of the data
Packer 2019 89,701 10x v2 653MB Several timepoints of embryo development A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution Science 2019. GSE126954 VisCello app for data exploration
Taylor 2019 65,450 10x v2/v3 217MB L4 larvae neurons selected via flow cytometry Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing biorxiv 2019. GSE136049 CeNGEN website Shiny R app to explore the data
Ben-David 2020 55,508 10x v2 145MB L2 larvae Whole-organism mapping of the genetics of gene expression at cellular resolution biorxiv 2020. - Gene count matrix was kindly provided by the authors on request
Taylor 2020 100,955 10x v2/v3 364MB L4 larvae neurons selected via flow cytometry Molecular topography of an entire nervous system. GSE136049 CeNGEN website Shiny R app to explore the data