in analysis (65 AD, 73 age and sex matched controls). The KAPA Stranded RNA-Seq Kit with RiboErase was used for library preparation. The library QC included a measurement of the average size of library fragments using the Fragment Analyzer (Advanced Analytical Technologies, IA, USA), and estimation of the total concentration of DNA by PicoGreen (Thermo Fisher Scientific, MA, USA). Raw reads were aligned to human genome 19 (hg19) using STAR aligner (Dobin et al., 2013). Quality control was assessed using RSeQC (Wang et al., 2012) and Picard (% GC, % duplicates, gene body coverage, unsupervised clustering, and library complexity, http://broadinstitute.github.io/picard/). The Picard “MarkDuplicates” option was used to flag and remove the duplicate reads. Gene quantification was performed with featureCounts using Gencode annotations. We filtered out all genes with lower expression in a substantial fraction of the cohort, with 18,463 genes with at least 1 CPM (counts per million) in at least 50% of the individuals; note that only these genes were carried forward in all subsequent analyses.
