Fig. 3. snRNA-seq2 reveals differences in gene expression between diploid and tetraploid hepatocytes.

A Scatterplot showing the higher number of genes per gene-length normalized counts (TPM) detected in 4n hepatocytes compared with 2n hepatocytes (left). The violin plot showing that the number of genes in 4n nuclei is 1.25-times higher than in 2n hepatocytes (right). B tSNE embedding of the hepatocyte cluster showing that 2n and 4n nuclei are clustered together. C MA plot showing average logarithmically transformed mean expression (x-axis) versus the log₂ fold change (y-axis) for pairwise comparison between 2n and 4n hepatocytes; 312 differentially expressed genes (DEGs) are depicted with crosses: 64 genes are upregulated in 2n nuclei (blue) and 248 genes are upregulated in 4n (orange). D Box plot of the coefficient of variation showing the transcriptional variability between 2n (n = 320) and 4n (n = 741) (left; two-sided Mann−Whitney U-test, *: p-value= 2.09e−14.). Box plots show the median coefficient of variation per ploidy status. The lower and upper ends of the boxes correspond to first and third quartiles, respectively, while the whiskers extend to minimum (first quartile minus 1.5 × the inter-quartile range (IQR)), and maximum (third quartile plus 1.5 × IQR). Data points beyond the whiskers are shown as individual points. Bar plot showing the higher number of highly variable genes (HVGs) that are not differentially expressed (non-DE) in 2n vs 4n (right).