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.