Additional file 1 of Distance-dependent inhibition of translation initiation by downstream out-of-frame AUGs is consistent with a Brownian ratchet process of ribosome scanning

Additional file 1: Fig. S1. High-throughput quantification of GFP intensities by FACS-seq. Fig. S2. Frame- and context-dependent inhibitory effects on protein synthesis by proximal dAUGs. Fig. S3. Codon adaptation index (CAI) and minimum free energy (MFE) do not significantly vary among Duo variants that contain dATGs at different positions. Fig. S4. The mRNA levels of dual-frame reporters and their respective controls measured by quantitative PCR. Fig. S5. High-throughput measurement of mRNA levels for dATG variants. Fig. S6. GFP intensities of dATG variants in the background of upf1Δ. Fig. S7. GFP intensity and mRNA level of the dATG variants in the 2A-inserted library. Fig. S8. Scatter plots showing GFP intensity and mRNA level in two biological replicates for yeast libraries. Fig. S9. GFP intensity and mRNA level for uATG variants in the background of hoΔ. Fig. S10. GFP intensity and mRNA level for uATG variants in the background of upf1Δ. Fig. S11. The optimization of the parameters in the Brownian ratchet scanning model using the MCMC algorithms. Fig. S12. The observed GFP intensities of dATG variants in FACS-seq experiments and the simulated GFP intensities under the Brownian ratchet scanning model. Fig. S13. Numbers of genes that harbor frame 0 or frame +2 dATGs at individual positions downstream of the aATG in the yeast or human genomes. Fig. S14. Numbers of genes harboring out-of-frame dATG for highly/broadly and lowly/narrowly expressed genes.