Fig. 2

Intronic reads account for a variable but substantial fraction of UMIs and stem from RNA. A Fraction of exonic and intronic UMIs from 97 primate and mouse experiments using various tissues (neural, cardiopulmonary, digestive, urinary, immune, cancer, induced pluripotent stem cells). Sequencing depth is indicated by shading of the individual bars. We observe an average of 21% intronic UMIs, with some level of tissue-specific deviations as, e.g., immune cells generally have higher fractions of intronic reads. B To determine if intronic reads stem from genomic DNA or mRNA, we extracted DNA from mouse embryonic stem cells (mESCs) and RNA from human-induced pluripotent stem cells (hiPSCs), pooled the two in various ratios (75, 50, 25, and 0% gDNA), and either treated the samples with DNase I (green) or left them untreated (gray). We then counted the percentage of genomic (=mouse-mapped) UMIs. This indicates that DNase I treatment in prime-seq is complete and that observed intronic reads are derived from RNA