Fig 1: Single-cell atlas and mesenchymal stem cell state characterization(A) Single-cell atlas of 204,883 cells across three tissues and four intervention groups. The tSNE plot is colored by cell type (warm colors, non-immune cell types; cold colors, immune cell types).(B and C) Single-cell atlas colored by tissue (B) and intervention group (C).(D) Re-clustering of ASCs in scWAT (left) and vWAT (right), colored by CytoTRACE-predicted differentiation stage (orange, less differentiated; gray, more differentiated). Ridge plots of individual ASC states are colored similarly.(E) Clustering of top ASC state-specific regulons (transcription factor with the number of regulated genes as a separate heatmap column) in scWAT (left) and vWAT (right). Shared regulons across the two depots are colored in blue. The heatmap is scaled by column.(F) Re-clustering of FAPs in SkM, colored by CytoTRACE-predicted differentiation stage (orange, less differentiated; gray, more differentiated). Ridge plots of individual FAP states are colored similarly.(G) FACS dot blot showing the sorting gates for Sca1+ and Sca1− FAPs from mouse triceps and gastrocnemius, with the percentages of the two populations labeled.(H) RNA staining of Pdgfra and Ly6a in triceps and gastrocnemius muscle.(I) Immunohistochemistry staining for PDGFRA, SCA-1, and LAMA4 (a marker for muscle fibers) in gastrocnemius muscle.(J and K) Top pathways (J) and regulons (K) enriched in Sca1+ and Sca1− FAPs. The pathway heatmap is colored by −log10 p value. The regulon heatmap is colored by activity score.See also Figure S3 Tables S2 and S3.