Extended Data Fig. 6: Ribosome profiling of Wnt and MYC mutated liver.
From: Hepatic zonation determines tumorigenic potential of mutant β-catenin
Ribosome profiling analysis comparing AAV8.TBG.Cre-treated wild-type (WT), Ctnnb1ex3/WT (B), R26LSL-MYC (M), and Ctnnb1ex3/WT;R26LSL-MYC (BM) livers 4 and 10 days post induction. a-e, Ribosome sequencing (Ribo-Seq) data. Biological replicates n = 3 per condition (time point and genotype). a, Principal component analysis (PCA) of Ribo-Seq data. Totals represents all sequenced cytoplasmic RNA, RPFs = ribosome protected fragments and represents sequenced RNA protected by ribosomes. b, c, Scatter plot presenting translational efficiency (TE) changes, colour scheme represents mRNAs translationally up-regulated (TE up, purple dots, padj<0.1 and TE log2FC > 0), down regulated (TE down red dots, padj<0.1 and TE log2FC > 0) WT livers were compared to either Ctnnb1ex3/WT (c) or R26LSL-MYC (d) livers at day 4 and 10. P values were calculated in DESeq2 using a two-sided Wald test, then multiple testing correction was applied using the Benjamini-Hochberg method. d, e, Scatter plot presenting translational efficiency (TE) changes and violin plots comparing day-4 and day-10 R26LSL-MYC (M) livers and Ctnnb1ex3/WT;R26LSL-MYC (BM) livers, coloured by TE groups from day 4 in panel c and day 4 in Fig. 1j. Boxplots represent the median (central line) and 25th and 75th percentiles of the data (box). Whiskers represent the maximum and minimum of non-outlier values within 1.5× the interquartile range. Data beyond the whiskers are outliers. f, Polysome profiles. Line and shaded areas represent mean and SD. Biological replicates n = 2.
