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.