Spatially variable gene detection

Spatially variable genes were identified using SpatialDE2 with default settings. Coordinates and full expression matrices of each brain were supplied, divided by cell type. To combine results from separate samples, a meta-analysis was performed on the raw P values from each sample, using Fisher’s method. The Benjamini & Hochberg correction for multiple comparisons was subsequently used and genes were considered spatially variable with an adjusted P value of < 0.01.