RNA was sequenced from the gray matter of dorsal lateral prefrontal cortex (DLPFC) of 542 samples, corresponding to 540 unique brains. These samples were extracted using Qiagen’s miRNeasey mini kit and the RNase free DNase Set. RNA was quantified using Nanodrop. The quality of RNA was evaluated by the Agilent Bioanalyzer. All samples were chosen to pass two initial quality filters: RNA integrity (RIN) score >5 and quantity threshold of 5 μg (and were selected from a larger set of 724 samples). RNA-Seq library preparation was performed using the strand specific dUTP method14 with poly-A selection. Sequencing was performed on the Illumina HiSeq with 101bp paired-end reads and achieved coverage of 150M reads of the first 12 samples. These 12 samples served as a deep coverage reference and included 2 males and 2 females of non-impaired, mild cognitive impaired, and Alzheimer’s cases. The remaining samples were sequenced with target coverage of 50M reads; the mean coverage for the samples passing QC is 95 million reads (median 90 million reads). The libraries were constructed and pooled according to the RIN scores
