Splicing accuracy varies across human introns, tissues, age and disease

Sonia Garcia-Ruiz, David Zhang, Emil K Gustavsson, Guillermo Rocamora-Perez, Melissa Grant-Peters, Aine Fairbrother-Browne, Regina H Reynolds, Jonathan W Brenton, Ana L Gil-Martinez, Zhongbo Chen, Donald C Rio, Juan A Botia, Sebastian Guelfi, Leonardo Collado-Torres, Mina Ryten

bioRxiv 2023.03.29.534370; doi: https://doi.org/10.1101/2023.03.29.534370

Repository

The 'splicing-accuracy-manuscript' repository contains the code used to generate all the analyses and figures produced for the manuscript Splicing accuracy varies across human introns, tissues and age.

1. 'manuscript_figures.R'

To produce the main and supplementary figures and tables using the 'Splicing' database, supplied for the manuscript "Splicing accuracy varies across introns, tissues, age and disease".

2. 'manuscript_ageing_figures.R'

Produces the main and supplementary figures and tables using the 'Age Stratification' database, supplied for the manuscript "Splicing accuracy varies across introns, tissues, age and disease".

3. 'manuscript_AD_figures.R'

Produces the main and supplementary figures and tables using the 'AD - control' SQLITE database (recount3 ID = SRP100948), supplied for the manuscript "Splicing accuracy varies across introns, tissues, age and disease".

4. 'manuscript_ENCODE_figures.R'

Produces the main and supplementary figures and tables using the 'ENCODE shRNA' SQLITE database, supplied for the manuscript "Splicing accuracy varies across introns, tissues, age and disease".

Supplementary Tables

All supplementary tables can be accessed through Zenodo using the DOI: 10.5281/zenodo.7732872

Databases

All SQLite databases used in the 'Splicing accuracy varies across human introns, tissues, age and disease' paper, can be freely downloaded from this website.

Tested Environments

The code included within this repository has been successfully tested on:

• Ubuntu version "16.04.7 LTS (Xenial Xerus)"
• Ubuntu version "22.04.2 LTS (Jammy Jellyfish)"

Acknowledgments

• All RytenLab members
• Aligning Science Across Parkinson's (ASAP)
• UCL Great Ormond Street Institute Of Child Health