To investigate glial cell composition across the caudate nucleus, DLPFC and hippocampus, we downloaded single-cell datasets for multiple brain regions26 similar to ours (that is, nucleus accumbens, DLPFC and hippocampus). To integrate the single-cell data for three brain regions, we modified the across-region analysis script from github.com/LieberInstitute/10xPilot_snRNAseq-human/blob/master/10x_across-regions-analyses_step02_MNT.R. Specifically, we cleaned the annotated datasets, removing the precalculated metrics. After this, we combined the data and normalized them with multiBatchNorm from the batchelor R package (v.1.17.2)80. Next, we subset the dataset specifically for annotated glial cells (that is, the microglia, astrocyte and oligodendrocyte lineage).
