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. Author manuscript; available in PMC: 2022 Jul 6.
Published in final edited form as: Cell Metab. 2020 Dec 9;33(2):379–394.e8. doi: 10.1016/j.cmet.2020.11.011

Figure 1. The cellular diversity of diseased kidney samples.

Figure 1.

(A) A schematic diagram illustrating the experimental procedure involving the digestion of whole-kidney tissue from 6 control and 2 FAN mice followed by sequencing using a 10x Genomics protocol. and transcriptomic analysis of 65,091 individual cells.

(B) Left, the UMAP of 29 distinct cell types identified by unsupervised clustering after excluding the proximal tubule cells. Right, the tSNE plot for the entire dataset including proximal tubule cells. Assigned cell types are summarized in right panel. GEC: glomerular endothelial cells, Endo: endothelial, Podo: podocyte, PT: proximal tubule, DLOH: descending loop of Henle, ALOH: ascending loop of Henle, DCT: distal convoluted tubule, CNT: connecting tubule, CD-PC: collecting duct principal cell, A-IC: alpha intercalated cell, B-IC: beta intercalated cell, CD-Trans: collecting duct transitional cell, Granul: granulocyte, Macro: macrophage, DC 11b+: CD11b+ dendritic cell, pDC: plasmacytoid DC, Baso: Basophile B: B lymphocyte, Treg: regulatory T cell, Tgd: gamma delta T cell, NK: natural killer cell.

(C) Bubble plots of cell cluster marker genes identified in control and FAN samples (size of the dot indicates the % positive cells, color indicates relative expression).

(D) Heatmap showing expression pattern of myeloid lineage markers.

(E) Gene expression feature plots of myeloid lineage cells projected onto the UMAP. Msrb1 (Methionine Sulfoxide Reductase B1): Granul, C1qa (Complement C1q A Chain): Macro, Cd209a (CD209 antigen-like protein A): DC 11b+, Cd24a (CD24a antigen): DC 11b-, Itgam (Integrin Subunit Alpha M): DC 11b+, and Fcer1a (Fc Fragment Of IgE Receptor Ia): Baso.

(F) Heatmap showing expression pattern of lymphoid lineage markers.

(G) Gene expression feature plots of lymphoid lineage cells projected onto the UMAP. Ccr7 (Chemokine C-C motif receptor 7): CD4 T, Foxp3 (Forkhead box P3): Treg, Il17re (Interleukin 17 receptor E): Tgd, Cxcr6 (Chemokine C-X-C motif receptor 6): NKT, Cd8a (CD8 antigen, alpha chain): CD8 effector, Klrb1c (Killer cell lectin-like receptor subfamily B member 1C): NK1–2, Cd7 (CD7 antigen): NK1 and Irf8 (Interferon regulatory factor 8): NK2