The composition of the tissue samples in terms of 8 broad cell type fractions—excitatory neurons, medium spiny neurons (also known as spiny projection neurons), interneurons, astrocytes, oligodendrocytes, ependymal cells, immune cells, and vascular cells—was estimated using deconvolution methods41. The principle behind this method is that the bulk expression of a gene for a tissue sample, here measured using RNAseq, is a convolution of the number of cells of each type comprising the sample and the average expression of the gene within the cells of each type. Because medium spiny/spiny projection neurons are not found in the cerebral cortex and excitatory neurons are not found in the striatum, 7 cell types were analyzed for each of these regions and shared cell types were used for across-region averages. A detailed description of this procedure can be found in41 and in Supplement 1.
