escherichia coli poly a polymerase kit  (New England Biolabs)

Journal: bioRxiv

Article Title: Benchmarking Tools for Identification of rRNA Modifications in Escherichia coli using Oxford Nanopore Direct RNA Sequencing

doi: 10.64898/2026.04.15.718756

Figure Lengend Snippet:

Article Snippet: We polyadenylated total RNA to enable direct RNA sequencing library preparation using the E. coli poly(A) polymerase kit (New England Biolabs, cat# M0276).

Techniques: Modification

Journal: bioRxiv

Article Title: Benchmarking Tools for Identification of rRNA Modifications in Escherichia coli using Oxford Nanopore Direct RNA Sequencing

doi: 10.64898/2026.04.15.718756

Figure Lengend Snippet: Heatmaps show the percentage of evaluated positions for which each tool reports a score, across 25 coverage depths (5x-1000×) on E. coli 16S rRNA (top) and 23S rRNA (bottom). Colour scale ranges from red (0%) through yellow (50%) to green (100%). Grey cells with em-dash indicate coverages where a tool failed to produce output and in the case of the tool nanoDoc, it indicates coverages not tested

Article Snippet: We polyadenylated total RNA to enable direct RNA sequencing library preparation using the E. coli poly(A) polymerase kit (New England Biolabs, cat# M0276).

Techniques:

Journal: bioRxiv

Article Title: Benchmarking Tools for Identification of rRNA Modifications in Escherichia coli using Oxford Nanopore Direct RNA Sequencing

doi: 10.64898/2026.04.15.718756

Figure Lengend Snippet: Performance of ten tools evaluated at 21 directional offsets (δ = -10 to +10 nt) from known modification sites on E. coli 16S and 23S rRNA at 1000× coverage. Negative δ values indicate upstream (5ʹ) displacement; positive δ values indicate downstream (3ʹ) displacement. (a) AUPRC across directional offset δ for each tool. Shaded bands indicate ±1 SD across replicates. The beige region highlights the ±2 nt range corresponding to the approximate 5-mer reader head context. (b) Row-normalised AUPRC heatmaps (each tool’s value scaled to its own maximum). White stars mark the peak offset per tool; the white vertical line indicates δ = 0 (true modification position). (c) Left: asymmetry index, defined as the difference between mean AUPRC over δ = +1 to +5 and mean AUPRC over δ = -1 to -5. Negative values indicate a 5ʹ bias (modification signal detected upstream of the true site). Right: peak offset δ that maximises AUPRC for each tool, shown separately for 16S (blue) and 23S (red) rRNA. Tools that peak at δ = 0 achieve exact positional localisation; tools peaking at negative δ values systematically mislocalise modification signals towards the 5ʹ direction.

Article Snippet: We polyadenylated total RNA to enable direct RNA sequencing library preparation using the E. coli poly(A) polymerase kit (New England Biolabs, cat# M0276).

Techniques: Modification

Journal: bioRxiv

Article Title: Benchmarking Tools for Identification of rRNA Modifications in Escherichia coli using Oxford Nanopore Direct RNA Sequencing

doi: 10.64898/2026.04.15.718756

Figure Lengend Snippet: Analysis performed at 1000× coverage on E. coli 16S rRNA (left) and 23S rRNA (right). (a) AUPRC as a function of symmetric tolerance window size (±0 to ±10 nt from known modification sites). Each line represents one tool; shaded bands indicate ±SD across biological replicates. The beige region indicates approximate 5-mer reader head context. (b) δ AUPRC heatmaps showing the change in AUPRC relative to exact-position evaluation (w = 0, vertical black line) for each tool and window size. Red indicates gains and blue indicates losses from the exact match. Stars mark the largest absolute change per tool. (c, left) Effective modification prevalence across window sizes, showing the fraction of positions counted as positive as windows expand. (c, right) Dumbbell chart comparing each tool’s AUPRC at exact position (open circles) with its peak AUPRC across all window sizes (filled circles), shown separately for 16S (blue) and 23S (red) rRNA.

Article Snippet: We polyadenylated total RNA to enable direct RNA sequencing library preparation using the E. coli poly(A) polymerase kit (New England Biolabs, cat# M0276).

Techniques: Modification