Extended Data Fig. 6: iBE does not induce off target RNA editing in organoids.
From: Generation of precision preclinical cancer models using regulated in vivo base editing
a. Schematic of experimental set up in iBE derived pancreatic organoids. Organoids were transduced and selected with GFPGO reporter (mScarlet+). Organoids maintained off dox were then split into dox conditions to induce BE expression for 4 days and then split again into + and – dox conditions for an additional day. b. Editing of organoids in each condition (OFF, D4, D8, and D4 sw) was quantified by flow cytometry, calculating the percentage of GFP+ cells within the mScarlet+ population. Data are presented as mean values ± s.e.m. One-way ANOVA with Tukey’s correction c. PCA analysis of RNA sequencing data from OFF, D8, and D4 SW organoids. Colors correspond to dox condition and shape delineates organoid replicate/mouse origin (n=3). d. Volcano plots from RNA-seq data comparing iBE pancreatic organoids culture on dox-containing media vs regular media. e. Off-target RNA editing analysis, processed as described for Supplementary Fig. 4. No significant differences in RNA variants were observed, n=3, one-way ANOVA with Tukey’s correction. Data are presented as mean values ± s.e.m. For all data shown, n=3 independent organoid lines/condition.
