Aging and senescence-associated transcriptional signatures in the mouse heart

This repository contains the analysis code and computational workflows used in the manuscript:

Authors

Aleksandra Aljakna Khan^1,6, Amalia Sintou^1,6, Yue Zhao^2,6, Antonios Somarakis², Harshpreet Chandok², Juliana Alcoforado Diniz², Ramalakshmi Ramasamy², Leon Frommer³, Sikander Hayat³, Mitch Kostich², Brian White², Paul Robson², Ron Korstanje¹, Matthew J. Mahoney^1,7, Nadia A. Rosenthal^1,7

¹The Jackson Laboratory, Bar Harbor, ME, USA
²The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
³Department of Medicine 2, RWTH Aachen University, Medical Faculty, Aachen, Germany
⁴Cardiovascular Research Institute and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
⁵Windreich Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA

⁶These authors contributed equally
⁷Co-corresponding authors

Correspondence:
Nadia A. Rosenthal, Matthew J. Mahoney The Jackson Laboratory
Bar Harbor, ME 04609, USA

This repository provides the computational analysis workflows supporting the results reported in the manuscript. It includes scripts for data preprocessing, statistical analysis, and generation of figures and tables. The repository is intended to ensure transparency and reproducibility of the reported analyses. Raw experimental data are not redistributed here; data access information is provided in the manuscript.

Repository structure:

.
├── data/          # input (not included) and processed outputs
├── src/           # preprocessing, analysis, statistics, utilities
├── requirements.txt
└── README.md

Software requirements include Python version 3.9 or higher and R version 4.2 or higher. Python package dependencies are listed in requirements.txt. R package dependencies are documented at the top of each R script.

R packages should be installed as indicated in the individual analysis scripts using install.packages or BiocManager::install.

Raw experimental data are not included in this repository due to size or data-sharing restrictions. Accession numbers and data availability details are provided in the manuscript. All processed data used in the analyses can be regenerated by running the provided scripts. Public reference datasets and annotations are either included or downloaded automatically by the scripts.

For questions regarding the analysis code, please contact:

Nadia A. Rosenthal
The Jackson Laboratory
Email: [email protected]

Matthew J. Mahoney
The Jackson Laboratory
Email: [email protected]