Conserved long-range base pairings are associated with pre-mRNA processing of human genes
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1. SupplementaryDataFile1.bed<br> 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<br> 14: CCR1<br> 15: CCR2<br> 16: structure in dot-bracket notation<br> 17: icSHAPE_delta_reactivity score<br> 18: ENSEMBL gene id<br> 19: NCBI gene name<br> 20: Presence of A-to-I editing sites (TRUE/FALSE)<br> 21: Presence of forked eCLIP peaks in both CCRs<br> 22: phastCons.score1<br> 23: phastCons.score2<br> 24: phastCons.score3<br> 25: Evidence from RIC-seq data<br> 26: Raw E-value (the product of R-scape E-values of all base pairs in the structure)<br> 27: E-value (adjusted with Benjamini-Hochberg correction)<br> 28: Free energy 2. SupplementaryDataFile2.bed<br> The full list of PCCRs, GRCh38 Human Genome assembly. The columns are as in SupplementaryDataFile1.bed. 3. SupplementaryDataFile3.tsv<br> RNA bridges, GRCh37 Human Genome assembly. The columns are as follows<br> 1: PCCR coordinates<br> 2: eClip peak coordinates<br> 3: exon coordinates<br> 4: RBP name<br> 5: NCBI gene name<br> 6: Change of the exon inclusion rate in RBP KD (delta PSI)<br> 7: PCCR id<br> 8: PCCR energy<br> 9: PCCR spread<br> 10: Difference of icSHAPE reactivity of CCR<br> 11: E-value<br> 12: number of PCCRs in the cluster 4. SupplementaryDataFile4.tsv<br> Exon loop-outs, GRCh37 Human Genome assembly. The columns are as in SupplementaryDataFile3.tsv. 5. SupplementaryDataFile5.bed<br> 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<br> 2: startA, start of part A<br> 3: endA, end of part A<br> 4: chrB, chromosome of part B<br> 5: startB, start of part B<br> 6: endB, end of part B<br> 7: Cluster ID<br> 8: Number Of Chimeric Reads
1. SupplementaryDataFile1.bed<br> 该文件包含GRCh37人类基因组组装版本下的全部PCCRs列表。该列表采用BED12+格式，其中第1至12列对应轨道枢纽（track hub），第13至28列为附加信息：<br>13: PCCR编号<br>14: CCR1<br>15: CCR2<br>16: 点括号表示法（dot-bracket notation）下的RNA二级结构<br>17: icSHAPE_delta_reactivity得分<br>18: ENSEMBL基因ID<br>19: NCBI基因名称<br>20: A-to-I编辑位点存在情况（TRUE/FALSE）<br>21: 两个CCR中均存在分支型增强型紫外交联免疫沉淀（eCLIP）峰的情况<br>22: phastCons.score1<br>23: phastCons.score2<br>24: phastCons.score3<br>25: RNA原位构象测序（RIC-seq）数据支持证据<br>26: 原始E值（结构内所有碱基对的R-scape E值的乘积）<br>27: 经Benjamini-Hochberg多重检验校正后的E值<br>28: 自由能<br>2. SupplementaryDataFile2.bed<br> 该文件包含GRCh38人类基因组组装版本下的全部PCCRs列表，列格式与SupplementaryDataFile1.bed完全一致。<br>3. SupplementaryDataFile3.tsv<br> 该文件包含GRCh37人类基因组组装版本下的RNA桥接结构（RNA bridges）数据集，各列信息如下：<br>1: PCCR坐标<br>2: eCLIP峰坐标<br>3: 外显子坐标<br>4: RNA结合蛋白（RBP, RNA Binding Protein）名称<br>5: NCBI基因名称<br>6: RBP敲低（KD, Knock Down）实验中外显子包含率变化量（ΔPSI）<br>7: PCCR编号<br>8: PCCR自由能<br>9: PCCR分布跨度<br>10: CCR的icSHAPE反应性差异值<br>11: E值<br>12: 簇内PCCR总数量<br>4. SupplementaryDataFile4.tsv<br> 该文件包含GRCh37人类基因组组装版本下的外显子环出（exon loop-outs）数据集，列格式与SupplementaryDataFile3.tsv完全一致。<br>5. SupplementaryDataFile5.bed<br> 该文件包含一套严格的分子内RIC-seq RNA接触数据集（承蒙薛教授惠赠，PMID:32499643），此类接触发生于片段A与片段B之间，各列信息如下：<br>1: chrA：片段A所在染色体<br>2: startA：片段A的起始位点<br>3: endA：片段A的终止位点<br>4: chrB：片段B所在染色体<br>5: startB：片段B的起始位点<br>6: endB：片段B的终止位点<br>7: 簇ID<br>8: 嵌合读段数量
