Extended Data Fig. 7: Characterization of CD organoids using scRNA-seq.

a, UB and CD transcription factors were abundant in clusters 0-4 identified in Fig. 3e, which contained >97% of the sequenced cells (b). c, Expression of markers associated with other differentiated nephron segments, including podocytes, proximal tubule, thick ascending limb of Henle’s loop (TAL), and distal convoluted tubule (DCT), was largely absent in the dataset. d, Mapping prediction scores from Azimuth analysis were notably higher in clusters 0-2, which contained the more differentiated principal cell populations, while the scores were fairly low in clusters 3 and 4. e, Similarly, the prediction scores for cells that mapped to alternative tubular fates (found almost exclusively in clusters 3 and 4) were generally much worse than those that mapped to collecting duct. f, UMAP of clusters 0-4 following random downsampling to 500 total cells that were used in Monocle trajectory analysis. g, The predicted lineage trajectory plotted by pseudotime, which corresponds to Fig. 3i.