The C. elegans transcriptome at single cell resolution

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Study Design

Explore cell-type specific gene regulationCompare cell types through differential expressionCharacterize new cell subtypesHelp chararacterize the worm transcriptome

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.

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.

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.

Help chararacterize the worm transcriptome

We also found many clusters of cells that we have not yet been able to subtype or assign to a precise spot in the worm cell lineage. For example, there are numerous neuron subclusters we have not yet characterized as one subtype or another.