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:

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

    Vito RT Zanotelli
    Matthias Leutenegger
    Xiao‐Kang Lun
    Fanny Georgi
    Natalie de Souza
    Bernd Bodenmiller

Mol Syst Biol. (2020) 16: e9798
https://doi.org/10.15252/msb.20209798

Please cite this article if you re-use any of the data or code.

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
       
• 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
       
• 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
       
• 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
       
• 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