Mapping snRNA-seq to Allen Brain Atlas

We mapped the mouse snRNA-seq gene expression profile to the mouse ISH atlas of the Allen Institute for Brain Science (http://mouse.brain-map.org) at the cluster level^{85 (link)}. The ISH data of each slice were summarized into voxel dataset, providing the gene expression profile of each voxel (Gene expression value X voxel). The brain structures file of each slice showed the anatomical annotation of each voxel (voxel X structures). First, we generated whole brain plots with only amygdala subnuclei annotation in each slice using brain structures file to select the proper coronal slice as reference image. We chose slice 37 to plot reference image, where we divided the amygdala into five subnuclei: BLA (Basolateral amygdalar complex), IA (Intercalated amygdalar nucleus), CEA (Central amygdalar nucleus), MEA (Medial amygdalar nucleus), and COA (Cortical amygdalar area). Then, we downloaded the ISH data of slice 37 to map gene expression on the reference image. We calculated the average expression value of the top 5 DEGs in each cluster and then, projected it on the reference image to infer the subnuclei distribution of clusters. (Only DEGs that appeared in the ISH coronal gene expression profile were retained).