Additional file 1 of SWISS: multiplexed orthogonal genome editing in plants with a Cas9 nickase and engineered CRISPR RNA scaffolds

Additional file 1: Figure S1. Flow cytometry of BFP-to-GFP conversion induced by PBE and the five PBEcs in rice protoplasts. Figure S2. Engineering the secondary structures of CRISPR RNA scaffolds. Figure S3. Flow cytometry of BFP-to-GFP conversion induced by various scRNAs and their cognate PBEcs in rice protoplasts. Figure S4. Frequencies of base editing of endogenous genes by different scRNAs and cognate PBEcs in rice protoplasts. Figure S5. Activities of esgRNA-2×MS2, esgRNA-3×MS2, sgRNA4.0, and esgRNA-2×com with cognate PBEcs in rice protoplasts. Figure S6. C-to-T editing frequencies generated by scaffold RNA-recruited APOBEC1 narrow-window variants in rice protoplasts. Figure S7. Flow cytometry of mGFP-to-GFP conversion induced by PABE and the three PABEcs in rice protoplasts. Figure S8. Flow cytometry of mGFP-to-GFP conversion induced by various scRNAs and their cognate PABEcs in rice protoplasts. Figure S9. Activities of the selected scaffold RNAs with their cognate PABEcs in rice protoplasts. Figure S10. Schematic of multiple sgRNAs assembly for SWISSv1.1 and SWISSv1.2. Figure S11. The distributions of deletion reads among the indel sequencing reads for SWISSv1.1, SWISSv1.2, and SWISSv3. Figure S12. Schematic of multiple sgRNAs assembly for SWISSv2 and SWISSv3. Figure S13. Comparison of the editing efficiencies between the SWISS systems and the individual genome editing tools (PBE, PBEc4, PABE-2, PABEc5, and paired nCas9). Figure S14. Simultaneous CBE, ABE, and DSB formation in rice plants. Table S1. The sgRNA sequences used to compare the activities of PBEcs and PABEcs. Table S2. The sgRNA sequences used for SWISSv1.1, SWISSv1.2, SWISSv2, and SWISSv3 editing in rice protoplasts. Table S3. Potential off-target sites analyzed for OsALS-T2, OsACC-T2, OsBADH2-Indels-sgL, and OsBADH2-Indels-sgR triple mutants. Table S4. Statistics of whole genome sequencing analysis. Table S5. Primer sequences used in this study.