Gene expression analysis

Following quality control (QC) analysis with the fastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc), reads were aligned using STAR ^[40] against the human genome assembly (NCBI build36 [hg18] UCSC transcripts). Reads that were identified as PCR duplicates using Samtools ^[41] were discarded. Gene expression levels were quantified as read counts using the featureCounts function ^[42] from the Subread package ^[42] with default parameters. The read counts were used for the identification of global differential gene expression between specified populations using the edgeR package ^[43]. RPKM values were also generated using the edgeR package. Genes were considered differentially expressed between populations if they had an adjusted p value (FDR) < 0.05.