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Fig. 1 | Genome Medicine

Fig. 1

From: Single-cell analysis reveals congruence between kidney organoids and human fetal kidney

Fig. 1

Single-cell RNA-seq profiling of human kidney organoids reveals expected and off-target populations. a tSNE plot revealing 13 distinct clusters (cluster O0 to cluster O12) identified from largest to smallest population as labelled. Clusters depicted in this figure have been referred to as organoid (O) followed by cluster number. Cluster identity indicated in colour key which includes select marker genes and highest ranking GO term for top 30 genes with positive log fold change values in each cluster. b Re-clustering of organoid nephron lineage cells from clusters O2 and O9 in a results in five nephron sub clusters as labelled. Cluster labels followed by marker genes expressed within the cluster. Clusters from this analysis have been referred to as organoid nephron (ON) followed by the cluster number. c, d Pseudotime trajectory analysis of organoid nephron cells supports a progression from nephron progenitor to podocyte, and proximal and distal nephron end points on different branches. Plot in c coloured by cluster identity in b. Plot in D coloured by Monocle state. e Expression of representative podocyte, nephron progenitor and tubular marker genes across the pseudotime trajectory coloured by Monocle state. f Dot plot representing key cell type marker gene expression within organoid nephron clusters. Dot size indicates proportion of cells in cluster expressing a gene, shading indicates the relative level of expression (low to high reflected as light to dark)

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