Correlation analysis of fold change of reads upon UV irradiation and the length, RPKM, and semi-extractive properties of lncRNAs. (A,B) Scatter plots illustrating the relationship between the length (A) or RPKM (B) of lncRNAs and the fold change of reads upon UV irradiation in HepG2, HEK293, Neuro2a, and HippCulture cells. Correlation coefficient (ρ) was calculated by Spearman's rank correlation analyses. Note that the length or RPKM did not exhibit a correlation with the fold change of reads upon UV irradiation. Blue lines represent regression lines. (C) Scatter plots illustrating the relationship between the fold change of reads in two different cell types (HEK293 [UV], HepG2 [UV]) and the fold change of reads after improved extraction (HeLa [semi]) compared with the fold change of reads upon UV irradiation (HepG2 [UV], HEK293 [UV]). Note that the y-axes HeLa (semi) showing the fold change of reads after improved extraction are reversed. Correlation coefficient (ρ) was calculated by Spearman's rank correlation analyses. Blue lines represent regression lines. (D) MA-plot of log2 fold change of reads upon improved extraction as a function of the relative abundance (log10 baseMeans) calculated by DESeq2 with an inverted y-axis. Light green dots represent lnRNAs, coral dots represent mRNAs, and dark green dots represent known functional lncRNA genes (fn lncRNA). Note that the extraction of NEAT1 is dramatically enhanced by the improved extraction, whereas other representative functional lncRNAs exhibited only mild, if any, enhancement. (E) Quasi-random beeswarm plots of log2 fold change of reads upon improved extraction (semi-extractability) and UV irradiation (UV sensitivity). Cell types used are indicated at the bottom of the plot. P-values are calculated by Wilcoxon rank sum test. Note that the y-axis for the semi-extractability in HeLa cell is reversed.
