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.
Using this app, you can investigate if there is allele-specific expression in F1s between N2 and 7 other strains at a given gene. See an overview across strains by default, or 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 also plots underlying gene and allele counts.
Our preprintdescribing the dataset and its analyses (cite to cite this app):
Stabilizing selection and adaptation shape cis and trans gene expression variation in C. elegans
Avery Davis Bell, Francisco Valencia, Annalise B Paaby. bioRxiv 2024.10.15.618466;
https://doi.org/10.1101/2024.10.15.618466