Extended Data Fig. 5: Unsupervised clustering analysis of iscRNA data identified DAM sub-populations.
From: Spotiphy enables single-cell spatial whole transcriptomics across an entire section
a, UMAP projection of 1,058 microglia extracted from iscRNA data produced by applying Spotiphy to mouse brain Visium data. Clusters are labeled with default clusters. b, Bar plots of microglia subtype proportions annotated from Fig. 4a for both WT and AD mouse samples. c, Volcano plot of differentially expressed genes (DEGs) among microglia in AD vs. WT. DEGs were determined using the iscRNA data. Volcano plot is generated in the same manner as described in Fig. 3. The genes highlighted are available in the CosMx panel and have been used to generate the signature scores in Fig. 4c–e. d, Heatmap of the expression of the top DEGs among microglia in WT and AD samples, respectively. e, Result of applying NetBID2 GSEA analysis to iscRNA data of microglia in AD vs. WT. f, beta-amyloid IHC staining of WT and AD samples. Scale bars: 500 μm. g, Quantification of beta-amyloid signals within different topographic regions of AD sample. Each barplot represents the average of fluorescence signal within each spot after overlaying the IHC image with Visium spot grid of the AD sample. The error bar represents the standard deviation. AD sample contains the following number of spots for each region: C&H (192), FT (144), TH (160), HY (233), STR (40), and n/a (2707).