Extended Data Fig. 5: T cell development pseudotime inference comparison.
a, DP to mature T cells with paired productive αβTCR in data from Suo et al. 20223, on the same UMAP embedding as in Fig. 4a and Supplementary Fig. 3c. The first two panels show the root cell and terminal states selected for pseudotime inferred directly from single-cell gene expression. The last panel shows the cell types. b, Top: pseudotime and branch probabilities inferred directly from single-cell gene expression on the same UMAP embedding as in a. Bottom: scatterplot of branch probability to CD8+ T against pseudotime. Each point represents a cell. c, UMAP of neighborhood GEX space, with the same neighborhoods as sampled in Supplementary Fig. 3c and UMAP embedding computed on gene expression pseudo-bulked by neighborhoods. Each point represents a cell neighborhood. The first two panels show the root cell and terminal states selected for pseudotime inferred from neighborhood GEX space. The last panel shows the cell types. d, Inferred pseudotime, and branch probabilities to CD8+ T and to CD4+ T respectively overlaid onto the same UMAP embedding in c.
