Interactive datasets from the Paaby lab: expression in wild C. elegans and their F1 progeny

To make our data and analyses easily available and, we hope, broadly useful, we have written interactive Shiny apps through which you can interrogate your favorite gene for its expression across several wild C. elegans strains in various conditions and crosses. The apps are linked and briefly described below; see our publications and/or get in touch for further detail.


Gene expression in 5 C. elegans strains x 3 RNAi treatments

Strains: N2, CB4856, JU1088, EG4348, QX1211. Treatments: par-1 RNAi, pos-1 RNAi, control vector

Using this app, you can see the normalized RNA counts per sample per gene, look up if there is differential expression between any two strain/treatment pairs, and see if there is overall differential expression across strains or in how strains respond to RNAi at that gene.

A writeup of the complete dataset and its analyses is in preparation; a link to the preprint/publication will be provided when available. Our preprint investigating expression variation on just the control data, with a focus on RNAi-related genes, is available on bioRxiv.

Go to the app!

Allele-specific expression data

Expression and regulatory divergence in wild C. elegans and their F1 progeny

Using this app, you can investigate if there is allele-specific expression in F1s between N2 and 4 other strains at a given gene. Make sure to select the strain you're most interested in using the drop down menu, and change strains with this menu to compare across them. The app will tell you if there were enough informative (variant-covering) reads at that gene in that strain to make allele-specific expression inferences, display the gene's classification in terms of inheritance mode and regulatory pattern, and show allele-specific expression and differential expression testing results. It further plots both underlying gene and allele counts and differential expression estimates from these counts.

A writeup of the dataset and its analyses is in preparation; a link to the preprint/publication will be provided when available.

Go to the app!