Extended Data Fig. 4: Single cell multiome analysis revealed that aged mito-Dendra2 High HSCs were characterized with HSC signature and oxidative phosphorylation genes.
(a) Violin plots showing differences in Surface Marker Overlap (SuMo) scores (upper) and HSC scores (lower) of young and aged mito-Dendra2 Low and High HSCs in each cluster. In the upper panel, P = 0, 2.99×10−209, 1.04×10−70, and 7.10×10−25 for Clusters 1, 2,3 and 4 (one-way Welch’s ANOVA). *P = 0, 0, 3.26×10−13, and 1.00×10−11 between aged mito-Dendra2 Low and High HSCs for Clusters 1, 2,3 and 4 (Games-Howell post hoc test). In the lower panel, P = 0, 1.90×10−172, 3.83×10−77, and 1.39×10−19 for Clusters 1, 2,3 and 4 (one-way Welch’s ANOVA). *P = 0, 3.77×10−14, 2.42×10−13, and 3.93×10−8 between aged mito-Dendra2 Low and High HSCs for Clusters 1, 2,3 and 4 (Games-Howell post hoc test). (b) Violin plot showing myeloid-biased (left) and lymphoid-biased (right) score. P = 0 and 0 (one-way Welch’s ANOVA). *P = 2.05×10−12 and 1.69×10−12 (Games-Howell post hoc test). (c) Violin plots showing differences in mRNA expression levels of ribosomal genes between aged mito-Dendra2 Low and High HSCs in clusters 1 (left) and 2 (right). *P = 1.13×10−261, 9.30×10−125, 1.93×10−264, 6.27×10−115, 9.12×10−227, 1.31×10−85, 1.62×10−273 and 2.65×10−150 from left to right, calculated by the Wilcoxon Rank Sum test, and adjusted based on Bonferroni correction with all genes using the Seurat package in R in a two-sided manner. (d) Gene set variation analysis (GSVA) using MitoCarta gene sets between aged mito-Dendra2 Low and High HSCs. Each dot represents one gene set. Two-sided adjusted P-values were calculated using the limma package. (e) Violin plots showing differences in mRNA expression levels of selected iron homeostasis genes between aged mito-Dendra2 Low and High HSCs. *P = 5.18×10−84 and 2.48×10−81 from left to right, calculated by the Wilcoxon Rank Sum test, and adjusted based on Bonferroni correction with all genes using the Seurat package in R in a two-sided manner.
