A portion of each tissue is processed for RNA and DNA extraction, quantification, and quality assessment. Extraction protocols that preserve both messenger RNA and microRNA are being used, and are available on the data portal. For measurement of gene expression, the LDACC analyzed approximately 1,000 samples using both microarrays (Affymetrix Human Gene 1.1 ST Array) and next-generation RNA sequencing (Illumina HiSeq 2000), during the pilot, to establish comparability of these methods using post-mortem tissue. The RNA-Seq uses a 76 base, paired?end Illumina TruSeq RNA protocol, averaging ~50 million aligned reads per sample. This read depth was selected to maximize sequencing value with the budget available, and should make it possible to accurately measure moderate- and some low-expressed transcripts, but will have limited ability to accurately quantify rare transcripts and splice isoforms. It should provide gene expression measurements equal to or more accurate than expression arrays and with a higher dynamic range (i.e. coefficient of variation <0.1 for at least 12,000 genes; Supplementary Figure 3). RNA-Seq allows one to evaluate allele-specific expression in heterozygous individuals, improving the power to identify cis
