Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer

Data and scripts to reproduce the analysis of Improved detection of colibactin-induced mutations by genotoxic E. coli in organoids and colorectal cancer by Rosendahl Huber, Pleguezuelos-Manzano, Ubels, Puschhof et al. published in Cancer Cell 2024.

Dependencies:

R version 4.2.2 and all packages listed in the dependencies.txt file.

Scripts

1. Study of colibactin-mutagenesis in pks-exposed organoids. Data folder contains .vcf files of organoid cells exposed to different pks⁺ E. coli strains

   • Figure_1_function.R and Figure_2_function.R scripts

2. Analysis of colibactin exposure in whole-genome cancer data

   • Figure_3.R, FigureS7A-D.R and makeFigure4.R

3. All scripts for training and running the random forest are in randomForest . To classify new data you need the bed files used for feature annotation and the trained models, both of which can be downloaded here

For any questions or comments about the code, please contact:

• Axel Rosendahl Huber: axel.rosendahl@irbbarcelona.org
• Joske Ubels: j.ubels-2@prinsesmaximacentrum.nl