Fig. 2: Integrated expression analysis of proteome-transcriptome trajectories over organoid culture duration.

a Scatterplot of RNA copy number (D21, D25, D29) and protein copy number with light blue color indicating high data point density and green for low density. Associated two-dimensional UniProt-keyword enrichment with basic functional terms, including ‘Differentiation’, ‘Glycolysis’, ‘Mitochondrion’, ‘TCA-cycle’ and ‘Protein-biosynthesis’ are highlighted in red. b Barplots of basic functional terms from 2D UniProt-keyword enrichment (from a). c Uniform Manifold Approximation and Projection (UMAP) representation of combined datasets from single cell transcriptomes of D25 untreated plus D24 TNFα-treated and vehicle control (VC) distinguished 14 cell type clusters. Visualization was carried out using Cell x Gene software; the contribution to the total cell number by each sample and cell type cluster is shown on the right. d The summed protein expression direction of corresponding transcript markers which were used to define the 14 cell clusters. Proteins were classified as overexpressed (FDR < 0.05 and log₂ fold-change >0), under-expressed (FDR < 0.05 and log₂ fold-change <0) or not differentially expressed (FDR ≥ 0.05) between D21 and D29. e Heatmap k-means clustering of bulk RNA and bulk protein of transcript cell-type markers for early glomerular epithelial 1 (EGE1), maturing podocyte (Podo), proximal tubular (PT) and stromal cells. The top 30 differentially expressed proteins D29 versus D21 (FDR < 0.01) were plotted. Source data are provided as a Source Data file.