Figure 1.

Protocol of workflow and quality control. (A) Protocol of workflow: from each healthy control donor, approximately ~100 neurons from the ventral (Ve) and dorsal (Do) tier of the substantia nigra (SN) were laser capture microdissected (LCM). Cells from 1 tier in each donor were pooled, RNA was extracted, and cDNA was obtained and prepared for sequencing, allowing us to compare the gene expression in vulnerable versus resistant neuronal populations and finally to perform functional analysis. 3rd = oculomotor nerve; GO = Gene Ontology; MP = Mammalian Phenotype; PL = pars lateralis. (B) Mapping rates as the percentage of reads mapping protein‐coding genes in each of the 14 available samples. The dashed line at 30% has been drawn to highlight samples with particularly lower mapping rates (healthy control [HC]1, 3, and 4 were excluded from further analysis). (C) Library complexity shown as the cumulative proportion of the library for the top 100 most expressed features/genes in each sample. (D) First 2 principal components (PC), which together explain ~45% of the variance. Label colors reflect the origin of the samples, whereas the intensity of the dots denotes the total number of counts in each sample (darker colors represent higher number of counts).