A collection of all C. elegans single cell RNA sequencing data
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 original data sources, for convenience a direct download link to the data in .h5ad format is provided.
|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|
About the data
Cao 2017 L2 Larva Dataset (reprocessed)
Cao and friends. Comprehensive single-cell transcriptional profiling of a multicellular organism. Science 2017.
This was the first scRNAseq C. elegans data to be published. The single cell matrices used here were a newer version that was reprocessed and re-annotated and kindly provided by Robert Waterston and colleagues.
The technology used was sci-RNA seq. Two experiments with C. elegans at the L2 larval stage were performed with labels and cell counts as below. Their annotations define 117 cell types.
Packer 2019 Embryogenesis Dataset
Packer and friends. A lineage-resolved molecular atlas of C. elegans embryogenesis at single-cell resolution. Science 2019.
In the paper supplements, the way the age of the embryos was defined is described as follows:
Around 250,000 L1 larvae were 29 plated onto four 100 mm petri plates seeded with NA22 bacteria and allowed to develop at 20 30 °C. As the worms reached the young adult stage, the population was closely monitored. When 31 about 20-30% of the adults had a single embryo in either arm of the gonad, worms were 32 subjected to hypochlorite treatment. The time hypochlorite was added to the worms was 33 considered t = 0.
They used 10x Genomics v2 chemistry to profile 89,701 cells, split as below. Their annotations define 183 cell types.
|Waterston_400_minutes||25875||400 minute synchronized embryos|
|Waterston_300_minutes||17168||300 minute synchronized embryos|
|Murray_b01||12129||mixed time point|
|Waterston_500_minutes_batch_2||11589||500 minute synchronized embryos, replicate 1|
|Waterston_500_minutes_batch_1||10532||500 minute synchronized embryos, replicate 2|
|Murray_r17||9363||mixed time point|
|Murray_b02||3045||mixed time point|
Taylor 2019 Neuron Dataset
Taylor and friends. Expression profiling of the mature C. elegans nervous system by single-cell RNA-Sequencing. biorxiv 2019.
This is the first data release of the C. elegans Neuronal Gene Expression Map & Network (CeNGEN). The aim of the project is to establish a comprehensive gene expression atlas of an entire nervous system at single-neuron resolution, described in the announcement publication. Their website is cengen.org.
As described in their website: We are performing 10x single-cell RNA-Seq on FACS-isolated neurons. Using 52,412 sequenced cells, 109/118 neuronal classes have been identified and computationally assigned to a cluster based on their gene expression fingerprint (93 confidently, 16 tentatively), and 9/118 classes have not been annotated yet.
They used 10x Genomics v2 and v3 chemistry to profile 65,450 cells from L4 stage larvae, split as below. Their annotations define 133 cell types.
|Experiment name||Cells||Strain||Method||Cell Types Targeted|
|acr-2||11719||CZ631||10xv3||Cholinergic ventral cord motor neurons|
|unc-3||6165||OH11746||10xv2||Ventral cord motor neurons|
|tph-1_ceh-10||4810||NC3580||10xv2||Serotonergic neurons and AIY, RID, CAN|
|ift-20||4056||OH11157||10xv2||Ciliated sensory neurons|
|nmr-1||2389||NC3572||10xv2||Motor circuit command interneurons|
Ben-David 2020 L2 dataset
Ben-David and friends. Whole-organism mapping of the genetics of gene expression at cellular resolution biorxiv 2020.
In this dataset 5 separate 10x v2 lanes were run with about 10,000 L2 cells on each, each batch is a replicate. Their annotations define 99 cell types.