A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients

This repository stores R scripts and annotation files to reproduce the analysis of the publication "A comprehensive atlas of fetal splicing patterns in the brain of adult myotonic dystrophy type 1 patients".

Prerequisites

Software:

• Git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git
• Conda: https://docs.conda.io/en/latest/miniconda.html

Data:

• Gene read counts for GTEx V8 can be downloaded from the public portal: https://gtexportal.org/home/datasets.
• Acquire raw RNA-Seq data for the following datasets:
  • Otero et al. (2021): GSE157428 (Navigate to the SRA Run Selector)
  • BrainSpan Atlas of the Developing and Adult Human Brain: phs000731.v2.p1*
  • Genotype-Tissue Expression (GTEx) project: phs000424.v8.p2*
• We recommend to use this pipeline for data preprocessing: https://github.com/MDegener/RNAseq-pipeline.

*protected data that requires authorized access by dbGaP

Getting started

1. Checkout this git repository: git clone https://github.com/cmbi/BrainDM1.git

2. Navigate to the repository: cd BrainDM1

3. Create and activate conda environment with all R package dependencies

conda create -p r-env -c r -c bioconda -c conda-forge git rstudio r-base r-tidyr r-dplyr r-stringr r-purrr r-ggplot2 r-corrplot  bioconductor-rtracklayer bioconductor-biomaRt bioconductor-edgeR r-matrixTests r-psych r-data.table r-dunn.test r-cairo r-statmod r-gtools r-ppcor r-argparse r-r.utils r-venndiagram r-cowplot r-gghighlight r-ggrepel  r-ggpubr

conda activate r-env

4. Unzip annotation files: gzip -d lib/SE.hg38.annotated.gff3.gz lib/gencode.v26.annotation.collapsed.gtf.gz

5. Run the following R scripts in this order:

   1. scripts/prepareSampleMetadata.R: Combines metadata for all selected samples into one table
   2. scripts/prepareSummarizedData.R: Creates a matrix of exon inclusion data for all selected samples
   3. scripts/comparePSI.R: Performs a group comparison of exon inclusion for all exon-skipping events

6. Now you can run any script in the scripts/figure or scripts/tables directory to reproduce the unedited content of the publication

Overview of directories and content

Directory	Content
lib	Misc files for annotation and selection of samples
results	Unedited output of the analysis scripts that are contained in the /scripts directory
scripts	Scripts to create summarized data and to reproduce all figures and tables of the publication