normalization data transformation protocol
Each sample was independently processed with Cufflinks in order to generate an initial transcriptome. We used the Cuffmerge tool to merge the private transcriptomes into a single reference, and at the same time annotated known genes and extended partial transcripts. This common transcriptome was used in a second pass with Cufflinks, which quantified each transcript and gene (known or novel) in each sample. The reference annotation used was based on the UCSC knownGenes table.