DepMap Datasets for WRN manuscript

Cancer Dependency Map (DepMap) data used for analyses in the manuscript "WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers" by Chan and Shibue et al. is packaged into an rds file.<br>This rds file contains a list of data matrices. All but one of these matrices ("MUT") have cell lines as rows and genes as columns (gene names are mapped to hgnc symbols). <br>This analysis uses the 18Q4 DepMap release. The latest Broad Institute DepMap data can be accessed at https://depmap.org.<br>Associated code for analysis is available at https://github.com/cancerdatasci/WRN_manuscript, and code and other materials can be accessed from https://depmap.org/WRN/<br>The rds file contains the following datasets:-<b>DRIVE</b>: Gene dependency scores from the Novartis DRIVE RNAi screen[1] processed using the DEMETER2 algorithm[2].<br>-<b>CRISPR</b>: Gene dependency scores from the Achilles CRISPR screen processed using the CERES algorithm[3].<br>-<b>GE</b>: Gene expression data (log2(TPM), protein coding genes only) [4]. <br>-<b>CN</b>: Log2 relative copy number [4].<br>-<b>MUT_HOT</b>: Binary matrix indicating which cell lines have hotspot missense mutations in each gene<br>-<b>MUT_DAM</b>: Binary matrix indicating which cell lines have damaging mutations in each gene<br>-<b>MUT_OTHER</b>: Binary matrix indicating which cell lines have other non-silent mutations in each gene<br>-<b>MUT</b>: Dataframe containing all mutation calls from the DepMap 18Q4 release [4]<br>-<b>RPPA</b>: CCLE protein abundance data using reverse-phase protein array [4].<br><b>References</b>[1] McDonald, E.R., et al., Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening. Cell. 170, 577-592 (2017).<br>[2] McFarland, J.M., et al., Improved estimation of cancer dependencies from large-scale RNAi screens using model-based normalization and data integration. Nat. Commun. 9, 4610 (2018).<br>[3] Meyers, R.M., et al., Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells. Nat. Genet. 49, 1779 (2017).<br>[4] Cancer Cell Line Encyclopedia Consortium, and Genomics of Drug Sensitivity in Cancer Consortium. Pharmacogenomic Agreement between Two Cancer Cell Line Data Sets. Nature. 528, 84–87 (2015).