The following manuscript describes ~200 differential exon expression estimates from RNA-seq data that were valided by qPCR. Another ~200 alternative splicing structures were validated by RT-PCR, gel electrophoresis, and Sanger sequencing. The RNA-seq data is a bit old now (2x42-mer Illumina GAII data). The samples consist of biological triplicates of a drug sensitive and resistant cell line (derived from the sensitive line). In addition to RNA-seq and qPCR, Affy Exon Arrays were also used to profile these samples.
Alternative expression analysis by RNA sequencing. Nature Methods. 2010 Oct;7(10):843-847.