Additional file 1 of Very long intergenic non-coding (vlinc) RNAs directly regulate multiple genes in cis and trans

Additional file 1: Table S1. Drugs used in SMS and Illumina RNAseq analyses. Table S2. DE mRNAs or vlincRNAs found in each drug treatment in the SMS RNAseq analysis. Table S3. Summary of the validation of the DE vlincRNAs by real-time PCR. Table S4. Numbers of mRNAs found to be co-expressed with each vlincRNA using either SMS or Illumina RNAseq. Table S5. Analysis of the concordancy of the two biological replicas (B1 and B2) of the RAT experiments. Table S6. Comparison of the aggregated RAT signal of different types of genes based on single-sided Wilcoxson Rank Sum Test. Table S7. The overlap between co-expression and the chromatin interaction datasets for top and botton half of expressed mRNAs. Table S8. Significance of the overlap between the co-expression and vlincRNA-chromatin interaction datasets with increasing RAT signal thresholds. Table S9. Overlap between the co-expression networks obtained after the separation based on the expression level and the chromatin interaction dataset for the SMS RNAseq platform. Table S10. Relative fold changes of the co-expressed transcripts in response to vlincRNA knockdown. Table S11. Genes in common between the co-expression and chromatin interaction datasets for each vlincRNA tend to be found consistently in drug and DMSO treatments. Table S12. The overlap between the co-expression and chromatin interaction datasets limited to the genes located on the same chromosomes based on top 50% and bottom 50% expressed mRNAs. Table S13. The top 100 GO terms enriched in the genes either negatively (Table S13.1) or positively (Table S13.2) co-expressed with the vlincRNAs. Table S14. Ratios of the normalized counts of each targeting gRNA vs the cognate non-targeting gRNA control in the mixed CRISPR/Cas13 cell lines subjected to various treatments. Table S15. Overlap between the co-expression networks and the chromatin interaction dataset for the Illumina RNAseq platform. Table S16. Overlap between the co-expression and the chromatin interaction datasets based on merged data for SMS and Illumina RNAseq platform. Table S17. The effect of vlincRNA knockdown on Illumina-based co-expression networks. Table S18. Coordinates of vlincRNAs and sequences of gRNAs used in the RAT and Cas13 knockdown cell lines.

附加文件1：表S1。用于单分子测序（SMS）及Illumina RNA测序（RNAseq）分析的药物。表S2。SMS RNAseq分析中，各药物处理组鉴定得到的差异表达mRNA（DE mRNAs）或超长基因间非编码RNA（vlincRNAs）。表S3。通过实时定量PCR（real-time PCR）验证差异表达vlincRNA的结果汇总。表S4。通过SMS或Illumina RNAseq分析，与每个vlincRNA共表达的mRNA数量统计。表S5。RAT实验的两个生物学重复（B1和B2）的一致性分析。表S6。基于单侧Wilcoxson秩和检验，不同类型基因的RAT信号汇总值比较。表S7。针对表达量排名前50%与后50%的mRNA，共表达数据集与染色质相互作用数据集的重叠情况分析。表S8。随着RAT信号阈值升高，共表达数据集与vlincRNA-染色质相互作用数据集的重叠显著性分析。表S9。基于表达量分层得到的共表达网络，与SMS RNAseq平台的染色质相互作用数据集的重叠情况。表S10。vlincRNA敲低后，共表达转录本的相对倍数变化。表S11。针对每个vlincRNA，共表达数据集与染色质相互作用数据集的共有基因，在药物处理组与二甲基亚砜（DMSO）对照组中均稳定存在。表S12。仅分析位于同一染色体上的基因时，基于表达量前50%与后50%的mRNA，共表达数据集与染色质相互作用数据集的重叠情况。表S13。与vlincRNAs呈负相关（表S13.1）或正相关（表S13.2）共表达的基因所富集的前100个基因本体（GO）术语。表S14。经不同处理的混合CRISPR/Cas13细胞系中，每条靶向向导RNA（gRNA）相对于同源非靶向gRNA对照的标准化计数比值。表S15。Illumina RNAseq平台的共表达网络与染色质相互作用数据集的重叠情况。表S16。整合SMS与Illumina RNAseq平台数据后，共表达数据集与染色质相互作用数据集的重叠情况。表S17。vlincRNA敲低对基于Illumina RNAseq的共表达网络的影响。表S18。RAT实验与Cas13敲低细胞系中使用的vlincRNA坐标及gRNA序列。