HnRNP C binding to inverted Alu elements protects the transcriptome from pre-mRNA circularization

Supplementary Tables for the research article submitted to Science Advances (manuscript number aea2351): "HnRNP C binding to inverted Alu elements protects the transcriptome from pre-mRNA circularization" Supplementary Table S1. Metadata and RNA-seq data files (EGAD00001004958 dataset) of subjects included in this study (healthy and Group 3 MB individuals) as reported in the International Cancer Genome Consortium (ICGC) Controlled Data database (https://ega-archive.org). Supplementary Table S2. List of circRNAs detected in RNA-seq data from EGAD00001004958 dataset using CircExplorer2 and CIRI. Supplementary Table S3. Differential expression analysis in Group 3 MB and AC of high confidence circRNAs detected in RNA-seq data from EGAD00001004958 dataset. Supplementary Table S4. Differential expression analysis in Group 3 MB and FC of high confidence circRNAs detected in RNA-seq data from EGAD00001004958 dataset. Supplementary Table S5. List of introns used for motif enrichment analysis (hg19). Supplementary Table S6. Gene expression analyses of RNA-seq data from EGAD00001004958 dataset (Group 3 MB vs AC and Group 3 MB vs FC). Supplementary Table S7. Genomic coordinates of EGAD00001004958-derived circRNAs tested in Group 3 MB cell lines. Supplementary Table S8. All circRNAs detected in control siRNA and siHNRNPC#1 D341 cells. Supplementary Table S9. Length and information of expressed genes’ introns and circRNAs’ flanking introns relative to Supplementary Figure S3D and Figure 4A (control siRNA and siHNRNPC#1 D341 cells). Supplementary Table S10. Number of inter-intronic IRAlu in expressed genes’ introns and circRNAs’ flanking introns relative to Supplementary Figure S3E and Figure 4B (control siRNA and siHNRNPC#1 D341 cells). Supplementary Table S11. Number of HNRNPC binding motifs in expressed genes’ introns and circRNAs’ flanking introns relative to Supplementary Figure S3F and Figure 4C (control siRNA and siHNRNPC#1 D341 cells). Supplementary Table S12. siHNRNPC#1 vs control siRNA AS analysis (D341 cell line). Supplementary Table S13. Differentially expressed genes in siHNRNPC#1 vs control siRNA gene expression analysis (D341 cell line). Supplementary Table S14. Differentially expressed circRNAs in siHNRNPC#1 vs control siRNA (+RNaseR treated samples) expression analysis (D341 cell line). 12 Supplementary Table S15. Features (coordinates, length, Alu, IRAlu, HNRNPC binding motifs) of circRNAs flanking intron sequences (control siRNA and siHNRNPC#1 D341 cells). Supplementary Table S16. Number of inter-intronic IRAlu (per kb) in circRNAs’ flanking introns relative to Figure 4B (control siRNA and siHNRNPC#1 D341 cells). Supplementary Table S17. Distance (bp) of HNRNPC binding motifs from Alu in circRNAs’ flanking introns. Supplementary Table S18. Distance (bp) of HNRNPC binding motifs from BSJs in circRNAs’ flanking introns. Supplementary Table S19. HNRNP C iCLIP peaks in Alu-containing introns at genome-wide level. Supplementary Table S20. HNRNP C iCLIP peaks in Alu-containing introns flanking the detected BSJs. Supplementary Table S21. HNRNP C-upregulated BSJs characterized by flanking introns containing hnRNP C iCLIP peaks in Alu elements. Supplementary Table S22. List of qPCR primers used in this study.提交至《Science Advances》（稿件编号：aea2351）的研究论文的补充附表，论文标题为《HnRNP C结合反向Alu元件保护转录组免受前mRNA环化》： 补充附表S1：本研究纳入的受试者（健康个体及第3组成髓母细胞瘤（Group 3 MB）患者）的元数据与RNA测序数据文件（EGAD00001004958数据集），相关数据已上传至国际癌症基因组联盟（International Cancer Genome Consortium, ICGC）受控数据数据库（https://ega-archive.org）。 补充附表S2：利用CircExplorer2与CIRI工具，在EGAD00001004958数据集的RNA测序数据中检测到的环状RNA（circRNA）列表。 补充附表S3：针对EGAD00001004958数据集RNA测序数据中检测到的高可信度环状RNA，开展第3组成髓母细胞瘤与前小脑（anterior cerebellum, AC）组的差异表达分析。 补充附表S4：针对EGAD00001004958数据集RNA测序数据中检测到的高可信度环状RNA，开展第3组成髓母细胞瘤与胎儿小脑（fetal cerebellum, FC）组的差异表达分析。 补充附表S5：用于基序富集分析的内含子列表（hg19参考基因组）。 补充附表S6：针对EGAD00001004958数据集的RNA测序数据开展基因表达分析（第3组成髓母细胞瘤与前小脑组对比、第3组成髓母细胞瘤与胎儿小脑组对比）。 补充附表S7：在第3组成髓母细胞瘤细胞系中验证的、源自EGAD00001004958数据集的环状RNA的基因组坐标。 补充附表S8：在对照小干扰RNA（small interfering RNA, siRNA）与siHNRNPC#1 D341细胞中检测到的全部环状RNA。 补充附表S9：对应补充图S3D与图4A的、表达基因内含子及环状RNA侧翼内含子的长度与相关信息（基于对照siRNA与siHNRNPC#1 D341细胞）。 补充附表S10：对应补充图S3E与图4B的、表达基因内含子及环状RNA侧翼内含子中内含子间反向Alu元件（inverted Alu, IRAlu）的数量（基于对照siRNA与siHNRNPC#1 D341细胞）。 补充附表S11：对应补充图S3F与图4C的、表达基因内含子及环状RNA侧翼内含子中HNRNP C结合基序的数量（基于对照siRNA与siHNRNPC#1 D341细胞）。 补充附表S12：siHNRNPC#1与对照siRNA的可变剪接（alternative splicing, AS）分析（D341细胞系）。 补充附表S13：针对siHNRNPC#1与对照siRNA的基因表达分析中筛选出的差异表达基因（D341细胞系）。 补充附表S14：针对siHNRNPC#1与对照siRNA（经核糖核酸酶R（RNase R）处理的样本）的差异表达环状RNA分析（D341细胞系）。 补充附表S15：环状RNA侧翼内含子序列的特征（坐标、长度、Alu元件、反向Alu元件、HNRNP C结合基序）（基于对照siRNA与siHNRNPC#1 D341细胞）。 补充附表S16：对应图4B的、环状RNA侧翼内含子中内含子间反向Alu元件的数量（每千碱基）（基于对照siRNA与siHNRNPC#1 D341细胞）。 补充附表S17：环状RNA侧翼内含子中，HNRNP C结合基序与Alu元件之间的距离（碱基对，bp）。 补充附表S18：环状RNA侧翼内含子中，HNRNP C结合基序与反向剪接连接位点（back-splice junctions, BSJs）之间的距离（碱基对，bp）。 补充附表S19：全基因组范围内含Alu元件的内含子中的HNRNP C单核苷酸分辨率紫外交联免疫沉淀（individual-nucleotide resolution UV crosslinking and immunoprecipitation, iCLIP）峰。 补充附表S20：环绕检测到的反向剪接连接位点的、含Alu元件的内含子中的HNRNP C iCLIP峰。 补充附表S21：包含HNRNP C上调的反向剪接连接位点，且该位点侧翼内含子的Alu元件中存在HNRNP C iCLIP峰的数据集。 补充附表S22：本研究中使用的实时定量聚合酶链反应（quantitative polymerase chain reaction, qPCR）引物列表。