Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing

RNA sequencing (RNA-Seq) allows an entire transcriptome to be surveyed at single-base resolution whilst concurrently profiling gene expression levels on a genome scale [1]. RNA-Seq is an attractive approach as it profiles the transcriptome directly through sequencing and therefore does not require prior knowledge of the transcriptome under consideration. An example of the use of RNA-Seq as a high-resolution exploratory tool is the discovery of thousands of additional novel coding and noncoding genes, transcripts and isoforms of known genes despite the prior extensive annotation of the mouse [2-4] and human genomes [5,6].