Code and pre-processed data for figure reproducibility of the manuscript 'Spatiotemporal dynamics of tumour microenvironment remodelling' Lisek*, Theurillat*, Pentimalli* et al., bioRxiv 2025

The raw data can be downloaded from GEO (after publication) and the scripts used to process the data ('data_processing.Rmd') and reproduce the main and supplementary figures ('figure_reproducibility.Rmd') are avaliable on GitHub (https://github.com/tpentim/spatiotemporal_dynamics/). The data includes 12 single-nuclei and 12 high-resolution spatial transcriptomics data (Open-ST) from a murine model of triple-negative breast cancer. Tumors have been profiled in 3 biological replicates from 4 timepoints (T0: control, T1-T3: tumor). 3 Open-ST data from xenograft tumor obtained throguh transplantation in immunocompetent mice of tumor cells alone (A), tumor cells + normal fibroblasts (B) and tumor cells + myofibroblasts (C) are also included. The processed single-nuclei and spatial objects generated with 'data_processing.Rmd' and the output of the 'figure_reproducibility.Rmd' in HTML format can be downloaded here.