Mapping mouse gonadal supporting cell cis-regulatory elements

Introduction

The following pipeline was created to analyse paired time-series ATAC and RNA-seq data of purified pre-granulosa and Sertoli cells from fetal gonads.

The analysis consists first in analysing the RNA-seq data by performing sex-differentially expressed gene analysis, embryonic stage differentially expressed genes using DESeq2, and GO term enrichment analysis of the obtained group of genes with ClusterProfiler.

Second, the ATAC-seq analysis consists in performing sex-differentially accessible open chromatin regions, embryonic stage differentially accessible open chromatin regions using DESeq2, and TF motif enrichment analysis of the obtained group of chromatin regions. Finally, we combine the RNA and the ATAC data to predict cis-regulatory regions and their target genes by correlation analysis with monaLISA.

We also performed ATAC footprint analysis with TOBIAS to predict TF bonding sites and recontruct gene regulatory networks.

How to run the pipeline

Install Conda

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
sh Miniconda3-latest-Linux-x86_64.sh
# Specify your installation directory

Clone the SupportingCRE git project

The following command downloads the last version of the pipeline in the SupportingCRE directory.

git clone [email protected]:IStevant/SupportingCRE.git

Install the Conda SupportingCRE environment

This installs a conda environment with R4.3.3, Snakemake, as well as all the dependencies necessary to run the pipeline. It can some time to install.

cd SupportingCRE
conda env create -f conda_env/SupportingCRE_env.yml

Install the R packages

Install missing dependencies

snakemake --core 1 -f install_packages

Run the full pipeline

snakemake --profile=slurm/ 

Run only the RNA-seq analysis

snakemake --profile=slurm/ -f RNA_analysis

Run only the ATAC-seq analysis

snakemake --profile=slurm/ -f ATAC_analysis