Fig. 3

Phiclust reveals subpopulations in a human fetal kidney data set that can be confirmed experimentally. a Force-directed graph layout and phiclust for the fetal kidney data set. Error bars indicate the uncertainty obtained by resampling the noise. Inset: UMAP of clusters with low, intermediate, and high values of phiclust. b UMAPs of the UBCD, SSBpr, and ICa clusters. Left: colors indicate sub-clusters. Right: colors indicate the log-normalized gene expression of the two indicated genes. One gene follows the red color spectrum, the other gene the green color spectrum. Absence of color indicates low expression in both genes, yellow indicates co-expression of both genes. c–e Immunostainings of week 15 fetal kidney sections. c UPK1A and KRT7 are expressed in the urothelial cells of the developing ureter (upper panel) and absent from the tubules in the adjacent inner medulla (lower panel). d PECs express CLDN1 and CAV2 (upper panel), as well as CLDN1 at the capillary loop stage and later stages (lower panel). MAFB staining is found in podocytes and their precursors in the SSB (lower panel). e CLDN11 and POSTN are expressed in interstitial cells visualized by immunostaining (upper panel). SULT1E1 is expressed in the interstitial cells surrounding the ureter (marked by UPK1A) and the tubule in the inner medulla (lower panel). Scale bars: 100 μm