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. Author manuscript; available in PMC: 2021 May 23.
Published in final edited form as: Nat Mater. 2020 Nov 23;20(2):260–271. doi: 10.1038/s41563-020-00853-9

Extended Data Figure 6. Analysis of single cell RNA datasets.

Extended Data Figure 6.

A. Variability within the datasets represented as a UMAP plot, coloured by transcriptional cluster, predicted cell cycle phase, main cell type and organoid conformation (clockwise from top left). B. Marker genes of main cells type, WT1 and PAX2 (nephron), PDGFRA (stroma) and SOX17 (endothelial). C. Proportion of each cell type in replicate conditions. P value (one-way ANOVA) indicated if p < 0.2. D. UMAP representation of nephron cells after re-transformation and clustering at higher resolution. Plots are coloured by transcriptional cluster, predicted cell cycle phase and organoid conformation. Cluster identities are stated. E. Marker genes identifying each cluster: GATA3 (distal), HNF1B (pre-tubule), CUBN (proximal), HNF4A (proximal), FOXC2 (pre-podocyte), MAFB (pre-podocyte / podocyte), PODXL (podocyte), SIX2 (progenitor), EYA1 (progenitor). F. Stromal UMAP coloured by transcriptional cluster, predicted cell cycle phase and organoid conformation (top to bottom). G. Markers of specific stromal clusters; SIX2, LYPD1, FOXC2, HOXA11 (Cluster 3, nephron progenitor-like), WNT5A, LHX9 (Cluster 7) and ZIC1 and ZIC4 (Cluster 10). H. Heatmap of scaled log counts per million of pseudo bulk counts from scRNAseq sets for the top 100 most significantly expressed genes identified in bulk RNAseq analysis (Figure 4). Each column represents a single cluster from a single replicate (e.g. R40, Nephron, Set 1). Hierarchical clustering of the limited gene set indicates that bulk-RNAseq changes are largely driven by changes in the nephrons and endothelial cells.