Fig. 1: Spatially resolved transcriptomic profiles of the multiple layers in human prefrontal cortex.
From: Stereo-seq of the prefrontal cortex in aging and Alzheimer’s disease
A The analysis pipeline of the study, with select figures created using BioRender (Created in BioRender. Gong, Y. (2024) https://BioRender.com/m56f734; Created in BioRender. Gong, Y. (2024) https://BioRender.com/l73a167; Created in BioRender. Gong, Y. (2024) https://BioRender.com/s92q855; Created in BioRender. Gong, Y. (2024) https://BioRender.com/c29s609). B The H&E staining, immunohistochemistry (IHC) staining for Aβ plaques (Aβ42; red) and nuclei (DAPI; blue), and layer clustering for NA (B01809A3), moderate (B01809C2), and severe (A02092E1) AD groups. The IHC experiment was conducted once. Scale bar for the upper panel of the IHC, 1,500 \(\mu m\), while the scale bar for the lower panel of the IHC, 100 \(\mu m\). C UMAP visualization of seven clusters across 12 samples, annotated by cortical layer I to VI (L1 to L6) and the white matter (WM). D Heatmap of the marker genes in each cortical layer and the WM. The x-axis represents six cortical layers and the WM. Colors represent the mean expression of the gene in each cortical layer and the WM. Violin and scatter plots illustrating the expression levels of previously identified (E) and unreported (F) layer marker genes in B01809A3. In the violin plot, the x-axis represents the layer specific markers, and the y-axis represents the cortical layers and the WM. The color represents the median gene expression in the cluster. For the scatter plots, six plots represent the distribution of the gene expression levels of the layer markers, respectively. The color represents the gene expression levels.
