DepMap 19Q3 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 625 cell lines, the RNAseq data includes 1,210 cell lines, and the copy number data includes 1,657 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. Additional Achilles processing information is published here https://www.biorxiv.org/content/10.1101/720243v1.full. 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.

version 2: uploaded a new version of CCLE_gene_cn.csv to correctly reflect released cell lines.