Fig. 3

Variance and sample clustering of normalized transcriptome expression values. Principal component analysis (PCA) of MRC-5 (spheres) and HFF (triangles) cell strains of specific PDs (indicated by color) treated with (filled-in symbols) and without (empty symbols) rotenone. The triplicates are clearly grouped. One of the HFF control sample triplicates of PD34 and PD58 were outliers and were excluded for the analysis, thus only 2 symbols are displayed. The outliers could be attributed to batch effects [116] and their removal from analysis has previously been documented [117]. Interestingly, samples treated with rotenone at low PDs cluster more likely with low PDs which were not treated. Triplicates (identical symbols) are clustered indicating small experimental errors. For young (low PDs) and old (high PDs) MRC-5 and HFFs, triplicates with and without rotenone group together indicating little variance due to rotenone treatment. However, for some intermediate PDs, the triplicates with and without rotenone differ strongly indicating transcriptome differences due to rotenone treatment