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.

Experiment name Cells
L2_experiment_1 35480
L2_experiment_2 507

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.

Experiment name Cells Description
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
eat-4 12743 OH9625 10xv2 Glutamatergic neurons
acr-2 11719 CZ631 10xv3 Cholinergic ventral cord motor neurons
Pan 9216 OH10689 10xv2 All 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
cho-1_2 3849 NC3579 10xv2 Cholinergic neurons
cho-1_2 3471 NC3579 10xv2 Cholinergic neurons
unc-47_2 3123 NC3582 10xv2 GABAergic neurons
ceh-34 2648 NC3583 10xv3 Pharyngeal neurons
nmr-1 2389 NC3572 10xv2 Motor circuit command interneurons
unc-47_1 1261 NC3582 10xv2 GABAergic neurons

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.

Experiment name Cells
F4_5 11633
F4_4 11464
F4_2 11424
F4_1 11336
F4_3 9651