Figure 3.

Characterization of ligand expression in sciatic nerve Schwann cells (see also Extended Data Fig. 3-1). Schwann cell transcriptomes from the injured, uninjured and neonatal nerve datasets (in Figs. 1E, 2C,E; also see Carr et al., 2019) were extracted, combined together, analyzed and batch-corrected using Harmony data integration and clustered in Seurat based on principal components. A, B, t-SNE visualizations of the combined Schwann cells (SCs), showing clusters (A) and datasets of origin (B). The clusters in A are also annotated based on marker gene expression (Extended Data Fig. 3-1A) and datasets of origin. Neonatal and 9 d refer to the FAC-sorted preparations at these timepoints while neonatal – set 2 and 9 d – set 2 refer to the cells prepared with myelin removal beads. C, A dendrogram showing hierarchical analysis of cell clusters from the combined Schwann cell dataset, with cluster identity numbers, annotations and colors as in A. D, Scatterplot showing differential correlation of single-cell transcriptomes from the combined Schwann cell dataset in A (individual colors represent different datasets) with bulk transcriptomes from uninjured adult versus neonatal Schwann cells on the x-axis and uninjured adult versus 9 DPI on the y-axis. E, Venn diagram showing the overlap of ligand mRNAs expressed in neonatal, injured and uninjured Schwann cell clusters from the combined Schwann cell dataset in A. Ligand mRNAs were considered to be expressed if they were detectable in 2% or more cells in any defined cell type cluster. F, t-SNE gene expression overlays of the combined Schwann cell data in A for Btc, Bdnf, Fgf5, Ucn2, Clcf1, and Gdnf. Cells that detectably express the ligand are colored blue, and the numbers correspond to the clusters. Injured Schwann cell cluster 3 (Inj.) is circled. G, Violin plots showing the relative expression of Bmp1, Gdnf, Shh, and Pdgfa in injured Schwann cluster 3 versus uninjured Schwann cell cluster 4 from the dataset in A. H, t-SNE gene expression overlays of the combined Schwann cell data in A for Igf1, Dhh, and Fgf1. Cells that detectably express the ligand are colored blue and the numbers correspond to the clusters. I, Violin plots showing the relative expression of Dhh and Fgf1 in injured Schwann cell cluster 3 versus uninjured cluster 4 from the dataset in A.