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.

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