calcium-PIEZO1

Jupyter notebook and Python code for the analysis of calcium influx in MCF-7 breast cancer cells via the PIEZO1 ion channel with varying cell morphology, as published in:

So, C.L., Robitaille, M., Sadras, F. et al. Cellular geometry and epithelial-mesenchymal plasticity intersect with PIEZO1 in breast cancer cells. Commun Biol 7, 467 (2024). https://doi.org/10.1038/s42003-024-06163-z

Overview

This repository contains:

• The Jupyter notebook calcium_PIEZO1.ipynb which runs the analysis and model fitting for the calcium signalling data, generating a subset of the results and figures for our study (Fig 2g-k and Supp Fig 2).

Installation and usage

To run the notebook:

1. Clone the repository.
2. Install the environment with conda using the included YAML file.

conda env create -f calcium_PIEZO1.yml

1. Download the data (see Data availability).
2. Set the datapath environment variables in the second code block of the notebook. The datapath must point to the file 200508_cytoo_mcf7_yoda_lean.csv.
3. Run all cells in order.

Data availability

Please refer to our published article for information on how to download the data.

References

Please see the companion paper linked above for details of the methods and packages used in this code.

Citing this code

If you use or adapt our code or methods in your research, please cite the companion paper linked above or as shown here in BibTeX format:

@article{so2024cellular,
  title={Cellular geometry and epithelial-mesenchymal plasticity intersect with PIEZO1 in breast cancer cells},
  author={So, Choon Leng and Robitaille, M{\'e}lanie and Sadras, Francisco and McCullough, Michael H and Milevskiy, Michael JG and Goodhill, Geoffrey J and Roberts-Thomson, Sarah J and Monteith, Gregory R},
  journal={Communications Biology},
  volume={7},
  number={1},
  pages={467},
  year={2024},
  publisher={Nature Publishing Group UK London}
}

This repository was archived on Zenodo upon acceptance for publication:

Questions

Please email michael.mccullough@anu.edu.au if you have questions about the code.