1. SupplementaryDataFile1.bed The full list of PCCRs, GRCh37 Human Genome assembly. The list is provided in BED12+ format, where columns 1-12 correspond to the track hub, and columns 13-28 contain extra information. 13: PCCR id 14: CCR1 15: CCR2 16: structure in dot-bracket notation 17: icSHAPE_delta_reactivity score 18: ENSEMBL gene id 19: NCBI gene name 20: Presence of A-to-I editing sites (TRUE/FALSE) 21: Presence of forked eCLIP peaks in both CCRs 22: phastCons.score1 23: phastCons.score2 24: phastCons.score3 25: Evidence from RIC-seq data 26: Raw E-value (the product of R-scape E-values of all base pairs in the structure) 27: E-value (adjusted with Benjamini-Hochberg correction) 28: Free energy 2. SupplementaryDataFile2.bed The full list of PCCRs, GRCh38 Human Genome assembly. The columns are as in SupplementaryDataFile1.bed. 3. SupplementaryDataFile3.tsv RNA bridges, GRCh37 Human Genome assembly. The columns are as follows 1: PCCR coordinates 2: eClip peak coordinates 3: exon coordinates 4: RBP name 5: NCBI gene name 6: Change of the exon inclusion rate in RBP KD (delta PSI) 7: PCCR id 8: PCCR energy 9: PCCR spread 10: Difference of icSHAPE reactivity of CCR 11: E-value 12: number of PCCRs in the cluster 4. SupplementaryDataFile4.tsv Exon loop-outs, GRCh37 Human Genome assembly. The columns are as in SupplementaryDataFile3.tsv. 5. SupplementaryDataFile5.bed A stringent set of intramolecular RIC-seq RNA contacts (provided by a courtesy of Prof. Xue, PMID:32499643). The contact are between part A and part B. The columns are as follows 1: chrA, chromosome of part A 2: startA, start of part A 3: endA, end of part A 4: chrB, chromosome of part B 5: startB, start of part B 6: endB, end of part B 7: Cluster ID 8: Number Of Chimeric Reads

Any questions or comments should be addressed to Dmitri Pervouchine d.pervouchine@skoltech.ru