Data and code for TARDBP exitron splicing paper

Takuma Yamagishi1), Shingo Koide1), Genri Toyama1), Aya Washida1), Yumi Yamada1), Ryutaro Hanyu1), Ekaterina Nadbitova1), Yuka Mitsuhashi Koike2), Takuya Konno1), Tomohiko Ishihara1), Taisuke Kato2), Osamu Onodera1) 2), Akihiro Sugai1)

1)Department of Neurology, Clinical Neuroscience Branch, Brain Research Institute, Niigata University, Niigata, Japan.

2)Department of Molecular Neuroscience, Resource Branch for Brain Disease Research, Brain Research Institute, Niigata University, Niigata, Japan. 

This repository contains data, analysis code, supplementary materials, and original uncropped blot images for the paper "Exitron splicing breaks TDP-43 aggregation-dysfunction spiral in ALS and FTLD".

Contents:

Data:

Raw data files used in the analyses (CSV format)

All data is contained in a single file named 'data.zip'

The ZIP file structure:

Separate folders for Figure 1 to Figure 5, and Supplementary Figure S1 to Supplementary Figure S9

Each folder contains the corresponding CSV files used for that specific figure

Processed data files directly used in figure generation (Excel format)

Analysis Code:

R Markdown (Rmd) files containing the complete analysis pipeline

These files include code for data processing, statistical analyses, and figure generation

Each section in the Rmd files corresponds to a specific figure in the main manuscript

Output:

PDF files generated from knitting the Rmd documents

These PDFs provide a readable format of the code along with its output

Original Blot Images:

Uncropped, full-length images of all blots used in the study

These images are provided to ensure full transparency and to allow for independent verification of our results

The R Markdown documents are organized by figure numbers as they appear in the main manuscript. They contain detailed R code that reproduces all analyses and generates the figures presented in the paper. The code utilizes various R packages for data manipulation, statistical analysis, and visualization.

To use this code:

Ensure all necessary R packages are installed

Verify that the data files are in the correct directory structure as indicated in the code

Run the R Markdown documents in the order presented

The inclusion of original, uncropped blot images allows for a complete assessment of the experimental data. These images are provided in their raw format, as captured by the imaging equipment, without any post-processing or cropping.

Note that while these materials allow for the reproduction of our analyses, readers should refer to the main manuscript for comprehensive interpretation of the results and their biological significance.

We encourage other researchers to use these resources for verification of our results or as a starting point for further investigations in the field of TDP-43 proteinopathies and TARDBP exitron splicing.

For any questions or issues regarding this data, code, or original images, please contact the corresponding author.

This work is licensed under CC BY 4.0. When using this data/code, please cite our paper.