Determining the effects of C10.36 mediated translocation of Surface Spliceosomal Complex (SSC) on alternative splicing in Ramos cells

High-throughput RNA sequencing was performed to assess the differential alternative splicing events in Ramos cells 24 h after treatment with either C10.36 or G24A (point mutant). The DEXSeq package (Anders et al., 2012) in R was used to analyze differential exon usage and intron retention (R Development Core Team (2008). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org.). Using GRCh37 GTF input and counting the number of unique ensemble transcript IDs from DEXSeq output resulted in 52360 unique transcripts that were further analyzed. Pairwise comparison across experimental conditions for exon usage and intron retention was performed. C10.36 specifically induced alternative usage of 548 exons across 365 different mRNAs as well as 29 differential intron retention events. Thus, ~0.6 % of the analyzed transcripts were substantially dysregulated by ASE. C10.36 treatment also resulted in differential expression of 55 RNAs of which only 35 are annotated, including mRNAs and non-coding RNAs.