An analysis studying aged mouse hematopoietic stem cells and megakaryocyte progenitors in an attempt to identify reasons for age-induced non-canonical platelet generation.
Hematopoietic Stem Cells (HSCs) are the source of our blood cells in both humans and mice. With a mouse model, the Forsberg lab at UC Santa Cruz has shown that as a mouse grows old, their HSCs begin to differentiate into a different kind Megakaryocyte Progenitors (the cells that govern platelet production), denoted 'non-canonical MKPs' or 'ncMKPs', as opposed to normally-behaving or 'canonical' MKPs. Non-canonical create higher amounts of platelets, and those platelets are also more prone to clotting (described as 'enhanced thrombosis' in the literature).
The combination of the weakening that comes with age with more aggressive, more likely clotting paints a concerning picture for any organism that may experience this, and can lead to an increase in heart disease.
This analysis hypothesizes that there is a transcriptomic or proteomic cause for ncMKP production and aims to find candidates for that cause.
Basic BASH shell proficiency is assumed. Mac users, this is built-in to your terminal. Windows users, please
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Terminal Access: Mac users use "Terminal". Windows users, please install WSL2 or another BASH-based terminal emulator of your choice (e.g. Git Bash).
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Git: used for version control, install here.
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uv: Our Python package manager. Ensures that code runs the same way, no matter the machine. Install it here.
To clone (download) this repository's contents, navigate to your parent directory of choice and run:
git clone https://github.com/akash-pandit/age-analysis
cd age-analysisTo download all python dependencies and configure your environment, run:
uv sync # yeah, its that easy.For Jupyter users: Launch jupyter with uv to ensure it uses the correct environment and navigate to one of the given URLs:
uv run jupyter lab