Relationship between the transcriptome and the proteome during MEDEP differentiation. (A) PCA of the mRNA expression in the 3 independent differentiation experiments using MEDEP cells (rlog: regularized log₂ of read count values for the 500 most variable genes). (B-C) Pearson correlation analysis of the mRNA (B) and protein (C) expression during MEDEP differentiation. Log₂ values of the expression values in transcripts per million reads (mRNA) or copy number per cell (proteins) were used for calculation. (D) Relationship between mRNA and protein expression, determined by Pearson correlation analysis, using the same expression values as in panels B and C. TE-corrected RNA values were obtained by multiplying RNA expression values by their TE factor obtained from Alvarez-Dominguez et al.³¹  Half-life–corrected protein values were obtained by dividing protein expression values by their half-life obtained from Schwanhäusser et al.³²  (E) Correlation between the modification of protein expression during TED and protein stability. (F) Both TE and protein stability contribute to the poor correlation between the MEDEP cell transcriptome and proteome during TED.