Non-strand specific, polyA+ selected RNA-seq libraries were generated using the Illumina TruSeq protocol. Libraries were sequenced to a median depth of 78 million 76-bp paired-end reads. RNA-seq reads were aligned to the human genome (hg19/GRCh37) using TopHat (v1.4) based on GENCODE v19 annotations. This annotation is available on the GTEx Portal (gencode.v19. genes.v6p_model.patched_contigs.gtf.gz, available at https://www.gtexportal.org/home/datasets). Gene-level expression was estimated as reads per kilobase of transcript per million mapped reads (RPKM) using RNA-SeQC on uniquely mapped, properly paired reads fully contained within exon boundaries and with alignment distances ≤ 6. Samples with fewer than 10 million mapped reads or with outlier expression measurements based on the D statistic were removed10.
