We collected published bulk brain RNA-seq samples from the AMP-AD consortium (AMP-AD MAYO, ROSMAP and MSBB)6, Braineac7 and the PsychENCODE consortium8 (Bipseq4, BrainGVEX4, CMC9, CMC_HBCC and UCLA_ASD4) from Synapse.org using the Python 2.7.5 package synapseclient v1.9.2 (ref. 75). The NABEC and GTEx datasets were retrieved from NCBI dbGaP and the TargetALS data were provided directly by the investigators. In addition, we collected brain bulk RNA-seq samples from the ENA and performed rigorous QC, resulting in 1,759 samples (Supplementary Note, Supplementary Fig. 1 and Supplementary Table 28). Combined with the other datasets, this yielded a total of 9,363 samples (Supplementary Table 1).
