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