Extended Data Fig. 1: Characterization of human adipogenesis models and comparison with primary cell proteomes.
(a) Fluorescence microscopy of cell models at early (day 0), middle (day 8), and late stages (days 12–14) of adipogenesis. Experiment repeated twice. LDs stained with BODIPY are shown in green, nuclei stained with DAPI are shown in blue, scale bar = 100µm (n = 3, experiment performed once). (b) qPCR of adipogenic marker genes at indicated time points. Values were normalized to the first detected time point. (n = 4, mean ± SD). (c) Hierarchical clustering of significantly altered proteins across initial stages of SGBS cell differentiation (n = 4, ANOVA, FDR < 10^(−2)). (d) Number of significantly altered proteins in the first 48 h of differentiation (n = 4, two-sided Student′s t-test, FDR < 10^(−2)). (e) Number of quantified protein groups during the differentiation of cell models and primary samples (n = 3 for cell models and n = 7 for primary samples, mean ± SD). (f) Number of proteins groups identified based only on unique peptides - analysis based on canonical not additional FASTA. (g) Violin plot of data points over the peak for each identified peptide in different cell models, average is indicated. (h) Number of proteins with the indicated CV values at each time point in each cell model. (i) Pearson correlations between samples. (j) Pearson correlations of the median protein intensities between each differentiated model and primary adipocytes (minimum two valid per condition, missing values imputed with 0). (k) Log2 LFQ intensities of adipogenesis markers in cell models.
