DepMap 20Q2 Public

This dataset contains the results of Avana library CRISPR-Cas9 genome-scale knockout (prefixed with Achilles) as well as mutation, copy number and gene expression data (prefixed with CCLE) for cancer cell lines as part of the Broad Institute’s Cancer Dependency Map project. We have repackaged our fileset to include all quarterly-updating datasets produced by DepMap.

The Avana CRISPR-Cas9 genome-scale knockout data has expanded to include 769 cell lines, the RNAseq data includes 1304 cell lines, and the copy number data includes 1745 cell lines. Please see the README files for details regarding data processing pipeline procedures updates.

As our screening efforts continue, we will be releasing additional cancer dependency data on a quarterly basis for unrestricted use. For the latest datasets available, further analyses, and to subscribe to our mailing list visit https://depmap.org.

Descriptions of the experimental methods and the CERES algorithm are published in http://dx.doi.org/10.1038/ng.3984. Some cell lines were process using copy number data based on the Sanger Institute whole exome sequencing data (COSMIC: http://cancer.sanger.ac.uk.cell_lines, EGA accession number: EGAD00001001039) reprocessed using CCLE pipelines. A detailed description of the pipelines and tool versions for CCLE expression can be found here: https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md.

v2 changes: The README file in version 1 was missing descriptions for the files Achilles_raw_readcounts_failures.csv and Achilles_logfold_change_failures.csv. Version 2 corrects this.

v3 changes: Reverted to the README file from v1, because there are no _failures.csv files

v4 changes: The CCLE_expression file was in TSV format, and now is in CSV format. RNAseq data have been altered for three cell lines (see README for more details).