Public-facing repo for our Nature Communications publication White, Radakovic et al. Nanopore sequencing of intact, aminoacylated tRNAs

Previously preprint manuscript: White, Radakovic et al.

Here you will find processed data and figures for generating the plots contained within the manuscript figures, in the subdirectories:

• data - pre-processed aa-tRNA-seq and acid northern blot densitometry
• rmd - R markdown files for making the plots
• figures - png files generated from the above rmd files
• ref - alignment reference files
• src - useful scripts for extracting read metrics from POD5 data using ONT's Remora API

Raw POD5 files are available from ENA, but the links on the page are not active. Please use the links in ena-urls.txt to fetch POD5s (using e.g. wget).

Note: while Figure 3 plots will currently render upon cloning this repository and running the markdown files in the contained R project, Figure 4 files require additional large files from Remora metrics extraction. These files are hosted on Zenodo at record 10.5281/zenodo.14194756

A complete protocol for the sequencing approach (including EDC-activation of the 3´ adapter for chemical ligation, and chemical ligation conditions) is available on Benchling here. This protocol version is fixed to Jan 2025 and reflects the library preparation approach used to generate the data in the publication.

A Snakemake analysis pipeline is available at https://github.com/rnabioco/aa-tRNA-seq-pipeline