Second, despite their apparent promiscuity, enhancers are more generally detected in a much smaller subset of samples than mRNA transcripts (Supplementary Figs 21, and 22a, b), consistent with cell line studies7 and the higher specificity of non-coding RNAs (ncRNAs) in general13. Facets in which we detect many enhancers typically also have a higher fraction of facet-specific enhancers (Supplementary Fig. 22c, d). Third, the number of detected expressed enhancers and mRNA transcripts is correlated (Supplementary Fig. 21b), but the number of detected expressed gene transcripts (>1TPM) is 19-34 fold larger than the number of detected enhancers with the cutoffs used. Noteworthy exceptions include blood and immune cells, testis, thymus, and spleen, which have high enhancer/gene ratios. Conversely, smooth and skeletal muscle and skin, bone and epithelia-related cells have low ratios. Differential exosome activity between cell types might affect these results, but there was no correlation between hMTR4 mRNA expression and the number of enhancers detected (Supplementary Fig. 22e, f).
