Fig. 5: The expression of Apoe and Clu across platforms and validation with RNAScope. | Nature Communications

Fig. 5: The expression of Apoe and Clu across platforms and validation with RNAScope.

From: Integrating single-cell and spatially resolved transcriptomic strategies to survey the astrocyte response to stroke in male mice

Fig. 5

A Visium d2, d10 and d21 sections show high Apoe gene expression that is specific to the d10 injury site. B UMAP plot of the 10X Chromium scRNA-seq data annotated with cluster 3 (peach, proximal astrocytes) and cluster 0 (navy blue, distal astrocytes) shows Apoe expression is localized to cluster 3 (proximal) astrocytes. C Histogram depicts tDISCO-derived TPM normalized gene expression (y-axis) of Apoe in GFAP+ cells (numbered 1-22, x-axis) from zones A (red), B (orange), C (light blue), and D (dark blue). D Representative images of Apoe and GFAP expression in uninjured (left column) and d10 stroke-injured brains (second from left column).The red dotted line in stroke-injured brains denotes the injured area as defined by GFAP staining. Red boxes show the location of the higher magnification images that correspond to the uninjured brain (i), and proximal (ii)- and distal (iii)- regions in the stroke-injured brain. Images are at 10x, scale bar = 500 µm. Higher magnification images show Apoe and GFAP expression in i) uninjured, (ii) proximal and (iii) distal astrocytes (colocalization is depicted by the pink overlap mask). Images are at 40X, scale bars = 20 µm, n = 3 mice. cc = corpus callosum. E-H Clu expression in Visium (E), 10X Chromium (F), and tDISCO (G) datasets. Representative images of Clu and GFAP expression in uninjured (left column) and d10 stroke injured brains (second from left column), and in i) uninjured, (ii) proximal and (iii) distal GFAP+ astrocytes (colocalization is depicted by pink overlap mask) (H). Images are at 40X, scale bars = 20 µm, n = 3 mice. cc = corpus callosum. Source data are provided as a Source Data file.

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