Fig. 1: Proteome of kidney organoids evolves with duration in culture.
From: An integrated organoid omics map extends modeling potential of kidney disease
a Volcano plot of proteomic differential expression analysis (log2 fold change of label-free quantification intensity comparing D29 with D21). Proteins are represented by dots and the black line illustrates the significance cut-off (two sided t test, FDR < 0.05 and s0 = 0.1). Red colored proteins meet the significance threshold. Examples of strongly regulated proteins are labeled. Blue colored and labeled dots represent proteins highlighted in (b). b Immunofluorescence imaging of sectioned kidney organoids showing expression of (top panel) podocyte markers nephrin (NPHS1) and synaptopodin (SYNPO), and (bottom panel) cell structure and differentiation markers smooth muscle actin (ACTA2) and platelet-derived growth factor receptor alpha (PDGFRA), plus nuclear marker DAPI, n = 3, representative images shown, scale bar: 50 µm. c Heatmap (maximum distance) of normalized protein expression (mean subtracted label-free quantification values (average of three replicates)) during organoid differentiation. The zoomed-in region expands on the clusters that undergo marked changes during differentiation. Five clusters (of size >25 proteins) were distinguished and are indicated with colored rectangles. These five clusters are shown in (d). d GO enrichment analysis of unbiased clustering (clusters >25 proteins) of proteins during organoid differentiation (D21–D29) (Fisher’s exact test, FDR < 0.05). Source data are provided as a Source Data file.
