aa-tRNA-seq

Public-facing repo for the preprint White, Radakovic et al.

Code and figures found here (November 2024)

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

Data availability

Complete sequencing data (including POD5 and FASTQ files) and classification models will be available at the NCBI Gene Expression Omnibus and Zenodo upon manuscript acceptance.

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

Library preparation protocol

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.