Spatial transcriptomics of C. elegans males and hermaphrodites

RNA tomography is a method in which cryo-sectioning and RNA sequencing are combined to create transcriptome wide gene expression maps. We have adapted this method for C. elegans and have generated high-resolution anteroposterior gene expression maps of four young adult males and four young adult hermaphrodites (Ebbing et al., submitted). Here, we provide these gene expression maps to the community for open exploration.

We provide gene expression profiles of males and hermaphrodites, per individual section (20 µm) per aggregated anatomic region. The gene expression maps can be explored by entering a gene name, which provides information on:

• Expression in the aggregated maps. Here, the individual expression maps have been aligned and merged into a single, regionalized expression map. The aggregated maps are more sensitive, but provide a lower resolution view of expression patterns along the anteroposterior body axis.
• Expression in the individual male and hermaphrodite expression maps, displayed as z-score normalized expression. TMP normalized expression is available as a download.
• Spatially co-expressed genes based on similarity in expression patterns at a user defined correlation threshold. The expression of co-expressed genes is shown graphically and all correlation coefficients can be downloaded in table format.

Reference: Ebbing, A.*, Vertesy, A.*, Betist, M., Spanjaard, B., Junker, J.P., Berezikov, E., van Oudenaarden, A., and Korswagen, H.C. Spatially-resolved transcriptomics of C. elegans males and hermaphrodites identifies novel fertility genes. Submitted.

Outline of the RNA tomography method

Example: nerve ring specific gene flp-1

Expression of flp-1 in aggregated regions

Expression of flp-1 in individual sections and spatially co-expressed genes