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. 2024 Jan 13;61(8):5628–5645. doi: 10.1007/s12035-023-03869-9

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — Increased abundance of neurons in the ExN11 cluster suggests increased neurogenesis upon exercise. A (left panel) UMAP plots highlighting the ExN11 cluster, split by the experimental conditions (exercise and control). B Dotplot showing significant GO biological process terms enriched among the top 50 genes differentially expressed between ExN11 and ExN1 clusters, and among the top 50 genes differentially expressed between the ExN11 cluster and the ODC and OPC clusters. C Partition-based graph abstraction (PAGA) graph for InN2, ExN11, and ExN1 clusters, with velocity-directed edges constructed from RNA velocity measurements. Edges denote either connectivities (dashed) or transitions (solid/arrows). D Box-plots showing a significant decrease in the proportion of developing cells (ExN11/InN2) and an increase in the proportion of mature granule cells (ExN1) upon exercise. Each dot indicates one sample (n = 4/4 for exercise and control samples). E Violin plots showing normalized expression of selected marker genes for radial glia/immature neurons/exercise-mediated neurogenesis. F Cell-type specific regulons for ExN11 cluster identified using the SCENIC workflow. The y-axis denotes the regulon specificity score (RSS) (with high RSS values indicating high cell-type/cluster specificity, and vice versa). The x-axis denotes the rank of each regulon within the selected cluster, based on the RSS. The top 5 ranked regulons for ExN11 are labeled on the plot, with the number of genes comprising each regulon indicated within parentheses. G Dot plot showing significant GO biological process terms enriched among the collective list of genes and transcription factors (TFs) making up the top 5 regulons, as indicated in the RSS-Rank plot above. H Combined gene-regulatory network plot with TFs specific to InN2 and ExN11 clusters, and their respective regulon genes (larger nodes represent genes/TFs that connect two or more regulon networks)