Fig. 1: Spatial transcriptomic profiles partition the brain into discrete anatomical regions.
From: Spatial transcriptomics of the aging mouse brain reveals origins of inflammation in the white matter
A Overview of ST workflow using the 10X Genomics Visium platform. B Representative Visium image of O2FB (top, n = 3419 spots) showing spatial transcriptional profiles colored by cluster-based annotation (bottom). C Heatmap of top ten marker mRNAs (count mean values) in young, middle-aged, and old (left) or male and female (right) groups unique to each region. D Allen Brain Atlas P5614 coronal section images from http://mouse.brain-map.org/static/atlas showing the spatial locations of the seven major regions identified in (C). The relevant links are: Isocortex: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=315&z=6. Hypothalamus: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=1097&z=6. Thalamus: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=549&z=6. OLF.CTXsp: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=698&z=6. https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=703&z=6. Fiber tract: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3927.9999804496765&zoom=-4&structure=1009&z=6. Hippocampus: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=1080&z=6. CNU/striatum: https://atlas.brain-map.org/atlas?atlas=1&plate=100960084#atlas=1&plate=100960084&resolution=20.94&x=5519.9993896484375&y=3904.8334765434265&zoom=-4&structure=623&z=6. E Visium images (top) and UMAP (bottom) visualization of seven major regions showing the expression of representative well-known region-specific marker mRNAs in an old female sample (O2FB). Numbers in the color scale reflect the number of UMIs detected for the specified mRNA for each spot. F Same as (E) except profiles generated using a non-cluster-based method, SpatialDE (see Methods). Illustration credit for parts of (A) goes to Endosymbiont GmbH, and BioRender. Sen, P. (2025) https://BioRender.com/u24a349. Source data are provided as a Source Data file.
