Cardiac Cell Composition during Heart Failure

Written by Brian Gural
README last updated on Aug 21st 2024

Project Summary

This project is meant to measure the degree of cardiac cellular remodeling that occurs in C57BL/6 mice during heart failure, and how those compositional changes mediate bulk gene expression changes. Additionally, through a cardiomyocyte-specific knock-out model, we define the cardioprotective effect of the α1-adrenergic receptors.

Prior research has established the role of α1-AR in cardiac mitocondrial function and postinfarct remodeling

All data collection was performed in the labs of Drs. Brian Jensen, Christoph Rau, and Mikayla Patterson.

Example Results

Reproducing the analysis

This pipeline was written with SLURM-execution in mind. To run this pipeline on a SLURM-compatible HPC, simply run:

bash snake.sh

Once the items remaining in the "To-Do" list have been finished, this should produce a copy of every figure, from the source data.

To do:

• Break scripts into functional units
• Make pipeline executable with Snakemake
• Containerize with Singularity or version control with .Renv
• Download SRA files
• Add .fastq pseudoalignment