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 under normal and embryonic knock-down conditions

Differential expression for five C. elegans strains, under control condition and following RNAi targeting embryonic genes par-1 and pos-1

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.

Our paper describing the dataset and its analyses (cite to cite this app):
Beyond the reference: gene expression variation and transcriptional response to RNAi in C. elegans
Avery Davis Bell, Han Ting Chou, Francisco Valencia, Annalise B Paaby. G3 Genes|Genomes|Genetics, Volume 13, Issue 8, August 2023.

A related paper that examines gene expression in the context of strain-wise differences in germline RNAi competence:
Diversification of small RNA pathways underlies germline RNA interference incompetence in wild Caenorhabditis elegans strains
Han Ting Chou, Francisco Valencia, Jacqueline C Alexander, Avery Davis Bell, Diptodip Deb, Daniel A Pollard, Annalise B Paaby. Genetics, Volume 226, Issue 1, January 2024.

Allele-specific expression

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 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.

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

Gene expression across 208 strains (CaeNDR data)

Expression estimates for each gene for 208 strains

Using this app, you can examine the expression of any given gene across 208 wild C. elegan strains RNA-sequenced by CaeNDR (Zhang et al 2022). The app shows the distribution of expression levels at the selected gene along with specific expression for samples in your strain of interest, the strain with the highest expression at this gene, and the strain with the lowest expression at this gene. Note, this app loads all data at once and therefore may be to load, but quick to change genes once loaded.

Paper describing RNA-seq data generation:
Zhang, G., N. M. Roberto, D. Lee, S. R. Hahnel and E. C. Andersen, 2022 The impact of species-wide gene expression variation on Caenorhabditis elegans complex traits. Nat Commun 13: 3462.

Our write up describing this app and its underlying data processing:
in preparation for microPublication Biology