Insights into rRNA processing and modifications in Archaea using Nanopore-based RNA sequencing

Felix Grünberger¹, Michael Jüttner, Robert Knüppel, Sébastien Ferreira-Cerca², and Dina Grohmann¹

¹ Department of Biochemistry, Genetics and Microbiology, Institute of Microbiology, Single-Molecule Biochemistry Lab & Biochemistry Centre Regensburg, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany

² Biochemistry III – Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053 Regensburg, Germany.

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About this repository

This is the repository for the manuscript “Insights into rRNA processing and modifications in Archaea using Nanopore-based RNA sequencing”.

The repository is currently actively developed.

Preprint

This work is based on our previous preprint: Exploring prokaryotic transcription, operon structures, rRNA maturation and modifications using Nanopore-based native RNA sequencing.

What can you find here

A description of the workflow using publicly available tools used to basecall, demultiplex, trim and map (direct cDNA) data and data preparation for modified base detection (using direct RNA) can be found in the pipeline section.

Downstream analysis, including

• quality control
• detection of rRNA processing sites and classification of rRNA intermediates
• Circular RNA detection
• Modified base detection
  are based on custom Rscripts that are also described in the pipeline section.

Data availability

Raw direct RNA data (gzipped raw FAST5 files) have been uploaded to the Sequence Read Archive (SRA) and are available under project accession number PRJNA632538 (WT run: SRR11991303, ∆KsgA run: SRR11991308).
Direct cDNA data are available at the European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena) under project accession number PRJEB57168. ERP142133 ERR10466882

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License

This project is under the general MIT License - see the LICENSE file for details