Additional file 2 of Alternative 3′ UTR polyadenylation is disrupted in the rNLS8 mouse model of ALS/FTLD

Supplementary Material 2: Additional file 2. Table S1. APAlyzer analysis of rNLS8 mice. Table S2. REPAC analysis of rNLS8 mice. Table S3. APAlyzer analysis of TDP-43ΔNLS mice. Table S4. REPAC analysis of TDP-43ΔNLS mice. Table S5. DAVID analysis of APA genes in rNLS8 mice. Table S6. APAlyzer analysis of mice targeted with TDP-43 ASOs. Table S7. REPAC analysis mice targeted with TDP-43 ASOs. Table S8. CLIP-seq analysis of mouse TDP-43 binding sites. Table S9. APAlyzer analysis of TDP-43 Tg mice. Table S10. REPAC analysis of TDP-43 Tg mice. Table S11. APAlyzer analysis of microglia from rNLS8 mice. Table S12. REPAC analysis of microglia from rNLS8 mice. Table S13. Gene expression of APA genes in rNLS8 mice. Table S14. Protein levels of APA genes from a proteomic database. Table S15. APAlyzer analysis of TDP-43(M337V) iPSC motor neurons. Table S16. REPAC analysis of TDP-43(M337V) iPSC motor neurons. Table S17. APAlyzer analysis of TDP-43(K263E) iPSC cortical neurons. Table S18. REPAC analysis of TDP-43(K263E) iPSC cortical neurons. Table S19. APAlyzer analysis of TDP-43 RNAi knock-down in human motor neurons. Table S20. REPAC analysis of TDP-43 RNAi knock-down in human motor neurons. Table S21. A comparison of APA genes identified by APAlyzer in rNLS8 mice with list of APA genes in iNeurons from 3′-end sequencing. Table S22. A list of APA genes identified by APAlyzer in rNLS8 mice with evidence of conservation in human disease models. Table S23. A table summarizing the methodological details and results for each set of RNA sequencing data utilized

补充材料2：附加文件2。表S1：rNLS8小鼠的APAlyzer分析结果。表S2：rNLS8小鼠的REPAC分析结果。表S3：TDP-43ΔNLS小鼠的APAlyzer分析结果。表S4：TDP-43ΔNLS小鼠的REPAC分析结果。表S5：rNLS8小鼠可变多聚腺苷酸化（Alternative Polyadenylation, APA）基因的DAVID功能注释分析结果。表S6：靶向TDP-43的反义寡核苷酸（Antisense Oligonucleotides, ASOs）处理小鼠的APAlyzer分析结果。表S7：靶向TDP-43的反义寡核苷酸处理小鼠的REPAC分析结果。表S8：小鼠TDP-43结合位点的紫外交联免疫沉淀结合测序（CLIP-seq）分析结果。表S9：TDP-43转基因（Transgenic, Tg）小鼠的APAlyzer分析结果。表S10：TDP-43转基因小鼠的REPAC分析结果。表S11：rNLS8小鼠小胶质细胞的APAlyzer分析结果。表S12：rNLS8小鼠小胶质细胞的REPAC分析结果。表S13：rNLS8小鼠APA基因的基因表达水平。表S14：蛋白质组数据库中APA基因的蛋白表达水平。表S15：TDP-43(M337V)诱导多能干细胞（induced pluripotent stem cell, iPSC）来源运动神经元的APAlyzer分析结果。表S16：TDP-43(M337V)诱导多能干细胞来源运动神经元的REPAC分析结果。表S17：TDP-43(K263E)诱导多能干细胞来源皮层神经元的APAlyzer分析结果。表S18：TDP-43(K263E)诱导多能干细胞来源皮层神经元的REPAC分析结果。表S19：人运动神经元中TDP-43 RNA干扰（RNA interference, RNAi）敲低样本的APAlyzer分析结果。表S20：人运动神经元中TDP-43 RNA干扰敲低样本的REPAC分析结果。表S21：通过APAlyzer在rNLS8小鼠中鉴定的APA基因与3′端测序获得的iNeuron APA基因列表的对比分析。表S22：通过APAlyzer在rNLS8小鼠中鉴定的、在人类疾病模型中存在保守性的APA基因列表。表S23：汇总所用各组RNA测序数据的方法学细节与分析结果的表格。