Article Figures & Data
Figures
- Figure 1. Oxford Nanopore Technologies direct RNA sequencing and GCU motif detection.
(A) Schematic showing how RNA molecules are directly sequenced with Oxford Nanopore Technologies, followed by basecalling of the signal data produced by changes in ionic current, mapping to a reference, and detection of modified bases. Adapted from “Nanopore Sequencing,” by BioRender.com (2022). Retrieved from https://app.biorender.com/biorender-templates. (B) Three most significantly enriched MEME suite motifs in the 10-nucleotide sequences surrounding the top 1,000 putative modifications detected by the Tombo 5-methylcytosine Alternative Model for B. malayi, D. ananassae, C. albicans, E. coli, A549 native RNA, and A549 in vitro transcribed RNA. The top five motifs are shown in Table S3.
- Figure S1. Histogram of A549 native RNA methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S2. Histogram of A549 in vitro transcription RNA methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S3. Histogram of B. malayi methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S4. Histogram of D. ananassae methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S5. Histogram of C. albicans methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S6. Histogram of E. coli methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S7. Histogram of SARS-CoV-2 native RNA methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S8. Histogram of SARS-CoV-2 in vitro transcription RNA methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S9. Histogram of curlcake synthetic sequence methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure 2. Methylated fractions predicted by the Tombo Alternative Model for 5-methylcytosine.
(A) Density plots of the methylated fraction at all 3-mers containing a central cytosine in native and in vitro transcription viral RNA. Cytosine positions were filtered for depth >10 and methylated fraction >0 in both in vitro transcription and native samples. Histograms are available in Figs S10 and S11. (B) Boxplot showing distributions of the methylated fractions detected by the Tombo 5-methylcytosine Alternative Model. The methylated fraction was extracted for cytosines with a depth >100 except in the lower depth Sindbis virus samples, where cytosines with a depth >10 were retained. Methylated fractions were grouped based on the non-GCU and GCU sequence context. Statistical significance based on P-value from a two-tailed Z test and Cohen’s d effect size.
- Figure S10. Histogram of Sindbis virus native RNA methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
- Figure S11. Histogram of Sindbis virus in vitro transcription RNA methylated fractions detected by the Tombo Alternative Model.
Results plotted with R v4.0.3 using a bin width of 0.025.
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