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. 2019 Nov 29;10:5462. doi: 10.1038/s41467-019-13382-0

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Mature kidney organoids from four different human iPSC lines contain major nephron cell classes. a Schematic of differentiation protocols for kidney organoids derived from human iPSCs by the JB and ML protocols (methods). Single-cell sequencing time-points as shown. b Table summarizing single cells profiled across four different human iPSC cell lines (AS, N1, N2, ThF) using two different protocols (ML, JB) across four time points (iPSC, Day 7 (D7), 15 (D15) and 29 (D29)). Replicates are indicated in parentheses. c t-SNE plot of composite single-cell transcriptomic profiles from all four iPSC D29 kidney organoids (left) and human adult kidney (right). Cluster color annotations as shown. d (left) Violin plots showing expression of canonical adult human kidney markers used to identify nephron clusters in D29 organoids: podocyte (NPHS2), proximal tubule (PT; LRP2), thick ascending limb/distal nephron (TAL; SLC12A1) and immature distal nephron (GATA3 + DT). Mesenchymal and off-target cells were also detected. (right) Violin plots of data-derived tubular markers revealed proximal to distal gradient of APOE expression, proximal marker SPP1, and distal markers WFDC2 and MAL. e Random forest classifier trained on D29 ML_ThF organoid gene expression profiles accurately predicted respective nephron cell classes in human first and second trimester fetal kidney (e, f) as compared to adult kidney (g). The Y-axis labels in each panel represent the annotated cell class in each human sample. The X-axis labels are predicted cell classes at D29 (ML_ThF organoids). The size and intensity of the red dot represents the % of cells in the Y-axis cell-types classified as the corresponding X-axis cell-class, e.g., all human adult podocytes are correctly classified as podocytes, while distal convoluted tubule (DCT) is predicted to be most similar to the GATA3 + DT organoid cell class.