The ASCOT study appeared in Nature Communications today. ASCOT is a new resource allowing researchers to visualize and query alternative splicing patterns in public RNA-Seq data. The resource is freely available at ascot.cs.jhu.edu.
To populate ASCOT, we used Snaptron to identify splice-variants across tens of thousands of bulk and single cell RNA-Seq datasets in human and mouse. In the study, we use this resource to identify alternative exons used only by a single neuronal subtype. We use datasets from ENCODE and GTEx to study the unique splicing patterns of rod photoreceptors and found that PTBP1 knockdown combined with overexpression of MSI1 and PCBP2 activates rod-specific exons in HepG2 liver cancer cells.
This work demonstrates how large-scale analysis of public RNA-Seq datasets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.
It was a pleasure to work together with Seth Blackshaw‘s group on this work. The work was led by Jonathan Ling, with help from Chris Wilks and Rone Charles in my lab. Congratulations to Jonathan et al!