A two-sided unpaired t-test was used to assess expression differences between conditions (PD, iLBD, and age-matched controls) and brain regions (R1–R6) in the AHBA, UKBEC, and PD microarray dataset. For GTEx, we used DESeq2 version 1.22.248. For the PD RNA-seq dataset, normalization and differential expression was done with ‘DESeq2’ R-package version 1.10.1, with age and sex introduced in the statistical model to take into account possible biases. Each analysis done with DESeq2 used a two-sided Wald test. The cut-off for differentially expressed genes was P < 0.05 (BH-corrected). For microarray experiments, the FC was interpreted as the difference in mean expression µB−µA, with µ as the mean expression in either group A and B. For RNA-seq experiments, FC is the log2 FC obtained from DESeq2.
