Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm.

ABSTRACT:

Background

RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon junctions have been developed in order to overcome this problem. We compare the performance of RNA-seq (Illumina HiSeq) and junction arrays (Affymetrix Human Transcriptome array) for the analysis of transcript splicing events. Three different breast cancer cell lines were treated with CX-4945, a drug that severely affects splicing. To enable a direct comparison of the two platforms, we adapted EventPointer, an algorithm that detects and labels alternative splicing events using junction arrays, to work a

SUBMITTER: Romero JP 

PROVIDER: S-EPMC6156849 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature