Supplementary Figure 3: Periodate-treatment enables selective cloning of animal miR and miR* species upon restrictive Ath-HEN1-directed methylation.
From: Cell-type specific sequencing of microRNAs from complex animal tissues
(a) Volcano plots show fold-change and associated p-Values (determined by DESeq2, see methods) for the indicated number (n) of abundantly expressed fly (red) or mouse (black) miRNAs in small RNA libraries generated as described in Fig. 2a from the indicated input ratios. True-positive miRNA-recovery rate (TPR) was determined from the number of abundantly expressed fly miRNAs detected in the respective libraries above cutoff (log2 fold-change >1; p-Value<10−3) relative to the 64 fly miRNAs recovered at a read depth of >10 cpm (na=64) in untreated 1:1 input libraries. False-positive miRNA-recovery rate (FPR) was determined from the number of mouse miRNAs above cutoff (log2 fold-change >1; p-Value<10−3). (b) As described in Fig. 2a, total RNA derived from Drosophila melanogaster (dme) S2hen1 cells expressing Ath-HEN1 was mixed with total RNA from mouse (mmu) embryonic stem cells at the indicated ratios (input ratio), followed by small RNA cloning before (-ox) and after (+ox) oxidation by periodate-treatment. This experiment was conducted in triplicate. Here we focus on the fraction of miR* strands mapping to annotated mouse (mmu miR) or fly miRNAs (dme miR). The number of abundantly expressed fly miR*s (>100 cpm in untreated 1:1 input ratio libraries) still detected after the respective dilutions at a read depth of >100 cpm is indicated in parenthesis. (c) Volcano plots show fold-change and associated p-Values (determined by DESeq2, see methods) for the indicated number (n) of miR* strands of abundantly expressed fly (blue) or mouse (black) miRNAs in small RNA libraries generated as described in Fig. 2a from the indicated input ratios. True-positive miRNA-recovery rate (TPR) was determined from the number of abundantly expressed fly miR* species detected in the respective libraries above cutoff (log2fold-change >1; p-Value<10−3) relative to the expected 64 fly miR* partner strands of miRs recovered at a read depth of >10 cpm (na=64) in untreated 1:1 input libraries. False-positive miRNA-recovery rate (FPR) was determined from the number of mouse miR* species above cutoff (log2 fold-change >1; p-Value<10−3).
