Extended Data Fig. 4: scRNA-seq label transfer and trajectory analysis.
From: Differentiating visceral sensory ganglion organoids from induced pluripotent stem cells
(a-f) UMAPs of representative markers for each cluster identified at VSGOs, VSN for SLC17A6, SC for MPZ, SGC for TRPM3, GP for FBLN5 and MKI67, EpPL for PAX2. (g) comparison of VSN proportions between VSGO and i-VSN, two-sided Mann-whitney’s U test (4 biological replicates /each group, mean ± SEM). (h) Expression matrixplot of genes among iVSN cultured days (x axis). (i) UMAP of mouse nodose ganglion and VSGOs. (j) List of gene membership among each Macrogenes. (k) Expression of VSN score 2 among each VSN subclusters. (l) Terminal states of trajectory analysis. (m) Directed partition-based graph abstraction (PAGA) cluster UMAP. (n, o) UMAP of pseudotime and latent time. (p) UMAP plots of random walks among each cluster. (q, r) Smoothed gene expression trends for VSN_1 (q) and VSN_2 (r). Along with each trends, driver genes for each cell states are presented.
