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.

附加文件1：补充表1。小鼠视网膜发育过程中总RNA测序（total RNA-seq）与核糖体测序（Ribo-seq）数据的读段数量汇总。补充表2。发育中小鼠视网膜中鉴定到的A-to-I编辑位点（A-to-I editing sites）汇总。注：“链（strand）”表示该位点所在的链，0代表负链，1代表正链。补充表3。所有重复样本中A-to-I编辑位点的测序深度汇总。补充表4。相邻时间点间差异编辑位点的汇总。注：“差异编辑水平（DE level）”表示如第3列所述的两个时间点间编辑水平的绝对变化量；“p值（p-value）”为REDITS工具用于评估编辑水平变化显著性的统计量；“dRES”表示编辑水平变化的方向。补充表5。发育编辑模式的聚类信息。注：“隶属度（Membership）”表示编辑位点归属于某一类别的模糊隶属程度。补充表6。视网膜标志物基因位点的聚类信息。补充表7。不同发育编辑模式对应基因的基因本体（GO）富集分析（GO enrichment analysis）汇总。注：“基因符号（geneID）”为GO条目所分析的基因符号。补充表8。发育中小鼠视网膜中鉴定到的可变剪接事件（alternative splicing events）汇总。补充表9。编辑位点与剪接事件的相关性分析结果。注：“最小距离（dis.min）”表示编辑位点与其配对剪接事件之间的距离。补充表10。差异翻译效率（differential translational efficiency, TE）基因汇总。注：“log2倍变化估计值的标准误（lfcSE）”表示log2倍变化估计值的标准误。补充表11。用于验证的编辑位点筛选列表。