Oxford Nanopore Direct RNA Sequencing datasets for detecting rRNA modifications in the Brassica oleracea mitoribosome

Oxford Nanopore Direct RNA Sequencing (DRS) was applied for the detection of rRNA modifications in the Brassica oleracea mitoribosome. A comparison between native rRNA transcripts and in vitro transcribed (IVT) rRNA transcripts that were devoid of any modification indicated systematic base-calling errors and/or variations in current intensities that led to the prediction of the modified nucleotides (Begik et al., 2018).

For Nanopore (DRS) library preparation, custom reverse transcription adapters (RTAs) containing Deeplexicon multiplexing barcodes (BC1, BC2 or BC3) were designed for sequence-specific ligation to the 3’-ends of B. oleracea mitochondrial rRNAs.

Basecalling and demultiplexing of ONT direct RNA sequencing data were performed by Guppy and Deeplexicon, respectively.

For the analysis and visualization of current intensities, a full description is available in the associated publication.

The Eventalign_18S.R Rscript was used to make the nanopore 18S signal analysis

The Eventalign_26S.R Rscript was used to make the nanopore 26S signal analysis

The raw data for the scripts are in the following folders:

- For 26S: 26S_Native.barcode01 and 26S_IVT.barcode03- For 18S: 18S_Native.barcode01 and 18S_IVT.barcode02

These folders contain the read alignment files output from minimap2 (in .bam format) and the eventalign files generated by the f5c software (in tsv format).

The FASTA folder contains the mitochondrial 18S and 26S rRNA gene reference sequence in fasta format