A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids - Dataset

This is the umbrella archive that contains all the datasets and code associated with: <strong>A quantitative analysis of the interplay of environment, neighborhood, and cell state in 3D spheroids</strong> Vito RT Zanotelli<br> Matthias Leutenegger<br> Xiao‐Kang Lun<br> Fanny Georgi<br> Natalie de Souza<br> Bernd Bodenmiller <em>Mol Syst Biol. (2020) 16: e9798</em><br> https://doi.org/10.15252/msb.20209798 <em>Please cite this article if you re-use any of the data or code.</em> Datasets: Brightfield plate images: Contains all plate acquisitions for the individual sphere plates before pooling 4 cellline experiment: p173: 10.5281/zenodo.3991929 p176: 10.5281/zenodo.3991931 Overexpression experiment: p161: 10.5281/zenodo.3991925 p165: 10.5281/zenodo.3991927<br> Slidescan images: Contains all fluorescent slidescan images of the cuts derived from the pooled spheroid sample blocks 4 cellline experiment: p173: 10.5281/zenodo.3991921 p176: 10.5281/zenodo.3991923 Overexpression experiment: p161: 10.5281/zenodo.4066430 p165: 10.5281/zenodo.3991919<br> Spillover acquisitions: Contains all spillover acquisitions associated with the two experiments: 4 cellline experiment: p173/p176: 10.5281/zenodo.3991945 Overexpression experiment: p161/p165: 10.5281/zenodo.3991947<br> Imaging mass cytometry acquisitions: 4 cellline experiment: p173: 10.5281/zenodo.3991937 p176: 10.5281/zenodo.3991939 Overexpression experiment: p161: 10.5281/zenodo.3991933 p165: 10.5281/zenodo.3991935<br> Processed data set: 4 cellline experiment: 10.5281/zenodo.3991942 Overexpression experiment: 10.5281/zenodo.4271917 Code: A snakemake pipeline to reproduce the analyses from this raw data can be found at: http://github.com/BodenmillerGroup/SpheroidPublication A version already containing all the containers can be found at: 10.5281/zenodo.4071861