Processed DepMap data (.h5mu)

Disclaimer

The DepMap data were generated and shared by the Broad Institute of Harvard and MIT and the Sanger Institute.

We reprocessed the data and packaged it in a single h5mu file for easier access and to reproduce analyses with Semi-supervised Omics Factor Analysis (SOFA).  Please see https://www.biorxiv.org/content/10.1101/2024.10.10.617527v3 for more details on how the data was processed and analysed.

Data Usage Policy

The Broad Institute publishes its data under the Terms and Conditions linked here.

The Sanger Institute publishes its data under the Terms and Conditions linked here.

The DepMap data  are provided under Creative Commons Attribution 4.0 license.

Contact [e-mail] or [e-mail] for more information

Please cite the following when using these data

Drug response: Gonçalves, E. et al. Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40, 835–849.e8 (2022). (https://figshare.com/articles/dataset/Pan-cancer_proteomic_map_of_949_human_cell_lines/19345397)

Proteomics: Gonçalves, E. et al. Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40, 835–849.e8 (2022). (https://figshare.com/articles/dataset/Pan-cancer_proteomic_map_of_949_human_cell_lines/19345397)

RNA-Seq: Garcia-Alonso, L. et al. Transcription factor activities enhance markers of drug sensitivity in cancer. Cancer Res. 78, 769–780 (2018). (https://cellmodelpassports.sanger.ac.uk/downloads)

Methylation: Iorio, F. et al. A landscape of pharmacogenomic interactions in cancer. Cell 166, 740–754 (2016). (https://www.cancerrxgene.org/gdsc1000/GDSC1000_WebResources/Home.html)

Mutation: Iorio, F. et al. A landscape of pharmacogenomic interactions in cancer. Cell 166, 740–754 (2016). (https://cellmodelpassports.sanger.ac.uk/downloads)

CRISPR-Cas9: Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021). (https://score.depmap.sanger.ac.uk/downloads)

Metadata for all cell lines was obtained from:

Gonçalves, E. et al. Pan-cancer proteomic map of 949 human cell lines. Cancer Cell 40, 835–849.e8 (2022). 

Pacini, C. et al. Integrated cross-study datasets of genetic dependencies in cancer. Nat. Commun. 12, 1661 (2021).