Using human brain single-cell RNA-sequencing data profiled from the dPFC from Mathys et al32, we examined the cell-type specific expression of the 19 significant genes from the PWAS of depression. First, we performed data preprocessing and transformation using the Seurat package version 3.1.265. Genes were removed if they had fewer than 3 counts in a cell, and cells were removed if they had unique feature counts over 2,500 or less than 200. The RNA counts were normalized and scaled using the NormalizeData and ScaleData functions. The data had 17,926 genes in 70,634 cells before and 17,775 genes in 53,083 cells after quality control and normalization. We then focused on the 5 main cell types provided by Mathys et al 2019 using FindMarkers function: excitatory neuron, inhibitory neuron, astrocyte, microglia, and oligodendrocyte. For the 19 depression causal genes, we performed differential expression analysis to compare their expression levels in one cell type versus the rest of the other cell types using Wilcoxon Rank Sum test to determine if they are highly expressed in a particular cell type. The data met the
