scATAC-seq and scRNA-seq Integration Analysis in Adult Mouse Brain

Overview

This repository contains the code and data for integrating and analyzing single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data from the adult mouse brain. The analysis pipeline is implemented in R and utilizes the Seurat and Signac packages for processing and integration.

Aim

The primary goal of this project was to learn and understand the integration of scATAC-seq and scRNA-seq data, along with the utilization of the Signac and Seurat packages. By following the tutorial provided in the Signac GitHub repository, I aimed to gain practical experience in bioinformatics pipeline development, data integration, and analysis.

Data Sources

The scATAC-seq and scRNA-seq data used in this analysis were obtained from the 10x Genomics website:

• scATAC-seq data:
  • Peak matrix: atac_v1_adult_brain_fresh_5k_filtered_peak_bc_matrix.h5
  • Cell metadata: atac_v1_adult_brain_fresh_5k_singlecell.csv
  • Fragments file: atac_v1_adult_brain_fresh_5k_fragments.tsv.gz
  • Index file atac_v1_adult_brain_fresh_5k_fragments.tsv.gz.tbi
• scRNA-seq data:
  • Raw data: Allen Institute
  • Pre-processed Seurat object: allen-brain-RDS

Repository Contents

• scatac-seq-adult-mouse-brain.Rmd: This R Markdown file contains the code for the integration and analysis of scRNA-seq and scATAC-seq data.
• scatac-seq-adult-mouse-brain.html: The rendered HTML output of the analysis script.
• README.md: This README file providing an overview of the project, its aim, data sources, and repository contents.

Requirements

• R version: 4.3.3
• R packages:
  • Seurat
  • Signac
  • Other required packages as specified in the analysis script.

Usage

To reproduce the analysis:

1. Clone or download this repository.
2. Ensure that the required data files are placed in the appropriate directory.
3. Open and run the scatac-seq-adult-mouse-brain.Rmd file in RStudio or any other compatible environment.
4. Follow the instructions provided in the analysis script to execute the analysis steps.

Acknowledgments

• The Stuart Lab for providing the tutorial on scATAC-seq and scRNA-seq integration using the Signac package.
• 10x Genomics for providing the scATAC-seq data used in this analysis.