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. 2021 Apr 15;12:2277. doi: 10.1038/s41467-021-22266-1

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© The Author(s) 2021

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. 4 — a Di-graph representing cell type and lineage divergence, as derived from Cicero trajectory inference. Nephron progenitors (NP), podocytes (Podo), intermediate stage (IM), proximal tubule (PT), loop of Henle (LOH), and distal convoluted tubule (DCT) are connected with their developmental precursor stages and represented by ascending numbering. Arrows represent cell differentiation along respective trajectories. Genes listed next to the trajectories were derived from analyzing gene enrichment of differentially assessible peaks (DAPs) between two stages. Genes colored red were derived from the opening DAPs between two stages, genes colored blue were derived from the closing DAPs between two stages, and genes colored green were derived from opening DAPs between two branches. Three important genes, Foxl1, Hnf4a, and Tfap2b are shown along with their cell type-specific accessibility peaks and immunostaining results. Peaks that were open during the development of specific cell types are shown in red boxes. Immunofluorescence staining of P0 mouse kidney shows FOXL1 in red in the proximal part (Pr) of late S-shaped bodies (cross) and in podocytes within primitive glomeruli (#); green staining denotes E-Cadherin, blue DAPI; Med, medial part of S-shaped body; Di, distal part of S-shaped body; UE, ureteric epithelium; images are representative of three independent experiments, scale bars = 25 µm. HNF4A and TFAP2B in human adult kidney samples (images CAB019417 and HPA034683, respectively, taken from the Human Protein Atlas version 19.3, http://www.proteinatlas.org⁸³, https://creativecommons.org/licenses/by-sa/3.0/) are visualized by immunohistochemistry in brown, scale bar = 25 µm. In addition, gene expression changes along the three trajectories of genes that were identified by GREAT analysis to be nearby chromatin closing and opening events demonstrated to be consistent to chromatin information, examples are visualized in the top right subpanel. b Heatmap showing normalized gene activity scores of lineage marker genes in the 15 developmental stages.