Differential analysis of Huh7.5 ADAR1 KO and Huh7.5 wt translatomes. (A) Schematic depiction of mRNA differential expression and polysome loading analysis. DESeq2 analysis was done with interaction design of mRNA type and cell line parameters for Huh7.5 ADAR1 KO and wt cells. As an example, we show the normalized read counts for the LEO1 gene that exhibits increased polysome loading in Huh7.5 ADAR1 KO cells in comparison to Huh7.5 wt polysomes (log2FC = −1.425749). Further examples of mRNA behavior leading to differential polysome loading are depicted in Supplemental Figure S07. (B) Volcano plot of differential mRNA loading onto polysomes. The plot shows DESeq2 results for mRNA changes in total RNA samples. Threshold for FC is set to 1.5 and threshold for adjusted P-value is set to 0.05. Genes passing both thresholds are in red, genes passing only the FC threshold are in green, genes passing only the adjusted P-value are in blue, genes not passing any threshold are in gray. (C) Scatter plot of differentially expressed genes and genes with differential polysome loading. Out of 18,366 genes from total RNA analysis, only 13,835 genes that also appear in the differential polysome loading analysis are shown. Differentially expressed genes (FC > 1.5 and adjusted P-value <0.05 in total RNA) are in blue, genes with differential polysome loading are in green, genes that are both differentially expressed and exhibit differential polysome loading are in red, remaining genes are in black (unchanged).
