A Cell Atlas of Worm

The C. elegans transcriptome at single cell resolution


In Cao et al. (Science, 2017) we reported single cell RNA-seq of C. elegans larvae at ~50x 'shotgun cellular coverage' using a combinatorial indexing approach (sci-RNA-seq).

Here, you can download and analyze the data for yourself.

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We have built this site to make our data as accessible as possible so that others can analyze it for themselves. The documentation describes how to download the data and load up the software required to work with it. We also describe how to perform some common tasks such as comparing cell types to find genes that distinguish them. All our analysis code is hosted in a GitHub repository, so if you find a problem with it you can submit an issue or contribute a patch.

Explore cell-type specific gene regulation

Our analysis in Cao et al. associated cells in the sci-RNA-seq data with 27 high-level cell types as well as several neuronal subtypes. You can use the code we provide here to find out how your favorite genes are expressed in each of these cell types.

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Compare cell types through differential expression

So far, we have confidently classified most of the cells in the Cao et al. dataset by major type, and you can extract complete gene expression profiles for each and compare them to one another.

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Characterize new cell subtypes

Our preliminary analysis shows that the worm contains cells, such as the ASE neurons, that are transcriptionally unique. That is, each animal contains a single cell that expresses a unique pattern of gene that no other cell shares. While we know the broad type of each cell, identifying the transcriptome signature of the many subtypes in the worm will be an ongoing project. You can dive into such analyses by reclustering the data or subsets of the data.

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Help chararacterize the worm transcriptome

We also found many clusters of cells that we haven't yet been able to subtype or assign to a precise spot in the worm cell lineage. For example, there are numerous neuron subclusters we haven't yet characterized as one subtype or another. We need your help! If you'd like to contribute to the annotation of the worm transcriptome, join this google group.

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