Fig. 1
Tissue-specific bulk RNA sequencing of MAPK/ERK-deficient renal progenitor populations. A Whole mount image example of a mouse kidney expressing HoxB7Cre-GFP in the ureteric bud (UB) epithelium and collecting ducts at E14.5. White scale bar represents 300 μm. B Example whole mount image of the cortical surface of a mouse kidney expressing Six2-TGC-GFP in the nephron progenitor/metanephric mesenchyme (MM) population at E13.5. White scale bar represents 150 um. C RNA-Seq was separately performed on E12.5 control (n = 4 kidneys) and MAPK/ERK-deficient UB (HoxB7Cre-GFP;Mek1fl/fl/;Mek2−/−, n = 4 kidneys) and E13.5 control (n = 3 kidneys) and MAPK/ERK-deficient nephron progenitors (Six2-TGC-GFP; Mek1fl/fl/;Mek2−/−; n = 3 kidneys). Among the total reads of 55,335 and 52,636 in UB and MM, respectively, 1403 genes in the UB and 6720 in the MM were identified to be significantly differentially expressed with a cutoff of Padj < 0.05. Further filtering with │log2fold change│≥ 1 revealed 1004 differentially expressed genes (DEGs) for UB and 5053 for MM. D Volcano plot and heatmap for DEGs between wildtype and dko populations in the UB (left). Similar to the UB, the volcano plot and heatmap for MM (right) demonstrate clear segregation of the control samples from those lacking MAPK/ERK (dko) activity in UB and MM populations. The most prominent DEGs are numbered in the plots and represent the following genes: 1, Ccdc141; 2, Ifgbp5; 3, Slc40a1; 4, Ccnd1; 5, Etv5; 6, Atp2b4; 7, Samd9I; 8, Scn3b; 9, Xkr4; 10, Hist1h3c; 11, Rpl19; 12, Hist1h1a; 13, Rpl41; 14, mt-Rnr2; 15, Rpsa; 16, Rpl8; 17, Gm28439; and 18, Hist1h4d. Significant DEGs in the volcano plots are marked as red dots with a statistical cutoff of Padj < 0.05 and a magnitude threshold of │log2fold change│≥ 1. Heatmaps show downregulated genes in blue and upregulated genes in red; color intensity corresponds to the degree of differential expression. E Venn diagram shows 362 shared genes with differentially regulated expression in both UB and MM datasets. F Venn diagrams depicting up-/downregulated DEGs in UB and MM populations. Among the 1004 UB DEGs, we identified 372 genes (37%) whose expression was downregulated and 632 genes (63%) which were upregulated. Among the 362 shared DEGs between UB and MM, 157 genes (43%) were downregulated, and 193 genes (53%) were upregulated. Interestingly, 12 genes (3%) were inversely expressed, with six genes upregulated and six genes downregulated. Out of 5053 MM DEGs, 2712 genes (54%) were downregulated, and 2341 genes (46%) were upregulated