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

This '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. "Splicing" Database - Paper figure generation

To produce the main and supplementary figures and tables made using the 'Splicing' database supplied for the manuscript "Splicing accuracy varies across introns, tissues and age", please use the functions provided within the R script "splicing_accuracy_manuscript_figures.R".

2. "Age Stratification" Database - Paper figure generation

To produce the main and supplementary figures and tables made using the 'Age Stratification' database supplied for the manuscript "Splicing accuracy varies across introns, tissues and age", please use the functions provided within the R script "splicing_accuracy_manuscript_age_figures.R".

To evaluate whether the expression levels of RNA-binding proteins involved in post-transcriptional processes Van Nostrand et at. 2020 are affected by the age of the sample donor across BRAIN tissues, please use the code provided within the R script: "splicing_accuracy_manuscript_age_figures.R" (function 'age_stratification_RBPs_affected_age').

3. "ENCODE shRNA" Database - Paper figure generation

To produce the main and supplementary figures and tables made using the 'ENCODE shRNA' database supplied for the manuscript "Splicing accuracy varies across introns, tissues and age", please use the functions provided within the R script "splicing_accuracy_manuscript_ENCODE_figures.R".

4. Supplementary Tables

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

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