Additional file 1 of Temporal landscape and translational regulation of A-to-I RNA editing in mouse retina development

Additional file 1: Supplementary Table 1. Summary of the number of reads for total RNA-seq and Ribo-seq data in mouse retina development. Supplementary Table 2. Summary of identified A-to-I editing sites in the developing mouse retina. Note that ‘strand’ represents the strand where the site is located, with 0 for the reverse strand and 1 for the forward strand. Supplementary Table 3. Depths of A-to-I sites across all replicates. Supplementary Table 4. Summary of differential editing sites between adjacent time points. Note that ‘DE level’ represents the absolute change of the editing level between the two time points, as stated in column3; ‘p-value’ represents the statistical measure by REDITs to evaluate the significance of the change in editing levels; and ‘dRES’ represents the direction of the change in editing levels. Supplementary Table 5. Clustering information of developmental editing patterns. Note that ‘Membership’ represents the fuzzy membership degree of editing sites belonging to the class. Supplementary Table 6. Clustering information of sites in retinal markers. Supplementary Table 7. Summary of the GO enrichment analysis of genes for different developmental editing patterns. Note that ‘geneID’ represents the gene symbols being analyzed presented in the GO term. Supplementary Table 8. Summary of identified alternative splicing events in the developing mouse retina. Supplementary Table 9. Correlation between editing sites and splicing events. Note that ‘dis.min’ represents the distance between the editing site and its paired splicing event. Supplementary Table 10. Summary of differential translational efficiency (TE) genes. Note that ‘lfcSE’ represents the standard error of the log2FoldChange estimate. Supplementary Table 11. List of editing sites selected for validation.