Comparison of RNA-seq and Microarray Platforms for Splice Event Detection using a Cross-Platform Algorithm [Junction Arrays]

In this study, we compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of splicing events. Three different cell lines were treated with CX-4945, a drug that severely affects splicing. To make a fair comparison, we developed EventPointer, an algorithm that detects and labels alternative splicing events in both junction arrays and RNA-seq. Common results and discrepancies between both technologies were validated or resolved by more than 200 PCRs. Three different triple negative breast cancer cell lines (MDA-MB-231, MDA-MB-468, SUM 149) treated with CX4945 and DMSO with 5 replicates. A total of 30 samples This submission represents 'junction arrays' component of study.