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。表S2：rNLS8小鼠的REPAC分析。表S3：Tar DNA结合蛋白43（TDP-43）ΔNLS小鼠的APAlyzer分析。表S4：TDP-43ΔNLS小鼠的REPAC分析。表S5：rNLS8小鼠中可变多聚腺苷酸化（Alternative Polyadenylation, APA）基因的DAVID分析。表S6：靶向TDP-43的反义寡核苷酸（Antisense Oligonucleotides, ASOs）处理小鼠的APAlyzer分析。表S7：靶向TDP-43的ASOs处理小鼠的REPAC分析。表S8：小鼠TDP-43结合位点的交联免疫沉淀测序（Cross-Linking Immunoprecipitation Sequencing, CLIP-seq）分析。表S9：TDP-43转基因（Transgenic, Tg）小鼠的APAlyzer分析。表S10：TDP-43 Tg小鼠的REPAC分析。表S11：rNLS8小鼠小胶质细胞的APAlyzer分析。表S12：rNLS8小鼠小胶质细胞的REPAC分析。表S13：rNLS8小鼠中APA基因的基因表达水平。表S14：蛋白质组数据库中APA基因的蛋白水平。表S15：TDP-43(M337V)诱导多能干细胞（induced pluripotent stem cells, iPSC）来源运动神经元的APAlyzer分析。表S16：TDP-43(M337V) iPSC来源运动神经元的REPAC分析。表S17：TDP-43(K263E) iPSC来源皮层神经元的APAlyzer分析。表S18：TDP-43(K263E) iPSC来源皮层神经元的REPAC分析。表S19：人类运动神经元中TDP-43 RNA干扰（RNA interference, RNAi）敲低实验的APAlyzer分析。表S20：人类运动神经元中TDP-43 RNAi敲低实验的REPAC分析。表S21：通过APAlyzer在rNLS8小鼠中鉴定的APA基因与3'端测序获得的诱导神经元（induced neurons, iNeurons）中APA基因列表的比较分析。表S22：通过APAlyzer在rNLS8小鼠中鉴定的、且在人类疾病模型中存在保守性的APA基因列表。表S23：总结所用各组RNA测序数据的方法学细节与结果的汇总表。