The Cancer Dependency Map (DepMap) Cancer Cell Line Encyclopedia (CCLE) Dataset

Description

This dataset consists of whole genome sequencing (WGS), whole exome sequencing (WES), and RNA sequencing files generated from ~1000 cancer cell lines described in Ghandi et al., 2019.

Update Frequency

occasionally (as additional sequencings are generated for publicly-releasible CCLE models)

License

https://grants.nih.gov/policy-and-compliance/policy-topics/sharing-policies/accessing-data/using-genomic-data

Documentation

https://github.com/broadinstitute/depmap-omics-ccle

Managed By

Cancer Data Science, Broad Institute

See all datasets managed by Cancer Data Science](https://cancerdatascience.org/), [Broad Institute.

Contact

https://forum.depmap.org

How to Cite

The Cancer Dependency Map (DepMap) Cancer Cell Line Encyclopedia (CCLE) Dataset was accessed on DATE from https://registry.opendata.aws/depmap-omics-ccle. Ghandi, Huang, Jané-Valbuena et al. Next-generation characterization of the Cancer Cell Line Encyclopedia. Nature 569, 503–508 (2019). https://doi.org/10.1038/s41586-019-1186-3

Usage Examples

Tutorials

• DepMap Omics CCLE data on the AWS Open Data Registry by Devin McCabe
  

Tools & Applications

• Cancer Cell Line Encyclopedia (CCLE) by Ghandi, Huang, Jané-Valbuena et al.
  
• The Cancer Dependency Map (DepMap) by Arafeh, Shibue, Dempster et al.
  

Publications

• Bridging the gap between cancer cell line models and tumours using gene expression data by Noorbakhsh, Vazquez & McFarland
  
• Genetic dependencies associated with transcription factor activities in human cancer cell lines by Thatikonda, Supper, Wachter et al.
  
• Integrated cross-study datasets of genetic dependencies in cancer by Pacini, Dempster, Boyle et al.
  
• Machine learning multi-omics analysis reveals cancer driver dysregulation in pan-cancer cell lines compared to primary tumors by Sanders, Chandra, Zebarjadi et al.
  
• Next-generation characterization of the Cancer Cell Line Encyclopedia by Ghandi, Huang, Jané-Valbuena et al.
  
• Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal by Krill-Burger, Dempster, Borah et al.
  
• The Network Zoo: a multilingual package for the inference and analysis of gene regulatory networks by Ben Guebila, Wang, Lopes-Ramos et al.
  
• The present and future of the Cancer Dependency Map by Arafeh, Shibue, Dempster et al.