Fig. 2: Biochemical processes underpinning senescence progress in MSC.

a Box plot showing average normalized expression value of genes related with DNA damage response pathway. b Dot plot showing selected feature genes from each cluster. Including genes down-regulated and up-regulated in DNA damage response. c Box plot showing average normalized expression value of genes related with mTOR signaling. d Representative Gene Ontology pathways showing enriched expression in Cluster 5. e Dot plot showing the proportion of MSCs expressing and the expression level of representative genes associated with ATF6 signaling, IRE1 signaling and PERK signaling. f Heatmap displaying the activities of regulons in each cell ordered across pseudotime trajectory generated by monocle, with regulons labels at right. g RNA velocity analysis revealing the direction of transformation and the inter-relationship of MSC subpopulations. h Heatmap showing the t-values of regulon activity derived by the generalized linear model (GLM, see methods), t-values representing activity change between the current developmental stage and the previous one. Only regulons with at least one absolute t-value > 20 are showed. Regulons are clustered based on their activation (green box) or inactivation (black box) pattern. For the box plots in a and c, each single cell was used as an individual sample and annotated in the figure with the color represented by each MSC cluster, the plot center, box and whiskers corresponding to median, IQR and 1.5 × IQR, respectively. In the dot plots, color represents the scaled expression values from Seurat RNA assay, the displayed values were non-batch corrected. For a and c, p values were determined by two-tailed Wilcoxon rank-sum test (n = 4621 biologically independent cells in C5; n = 3409 biologically independent cells in C6; n = 13,105 biologically independent cells in C7).