Isoform expression profiles in immortalized B-cells (LCL) in response to interferon stimulation

Type I interferon (IFN) plays an important role in the innate immune response through inducing IFN-stimulated genes (ISGs) for innate immune response. However, how alternative splicing events, especially over time, affect the function of ISGs remains poorly understood. In this study, we generated a novel isoform annotation for IFN-a-stimulated human B-cells, called isoISG, using two long-read sequencing platforms (PacBio and ONT). To examine the variation in interferon responses among individuals at an isoform level, we obtained additional short-read RNA-seq data of LCLs and examined the detailed profiles of isoform switching to understand the impact of alternative splicing on ISG function in IFN stimulation responses. We further examined genetic variants influencing the ratio of isoforms (splicing QTLs) that are associated with GWAS.