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).

Cancer Dependency Map (DepMap)数据集已被用于Chan与Shibue等人发表的论文《WRN解旋酶是微卫星不稳定癌症中的合成致死靶点》中的分析工作，该数据集已打包为rds格式文件。<br>该rds文件包含一组数据矩阵。除名为"MUT"的矩阵外，其余所有矩阵均以细胞系为行、基因为列（基因名称已映射至人类基因命名委员会（HGNC）符号）。<br>本分析采用18Q4版DepMap数据集。博德研究所（Broad Institute）最新的DepMap数据集可通过https://depmap.org获取。<br>相关分析代码已开源至https://github.com/cancerdatasci/WRN_manuscript，配套代码及其他材料可通过https://depmap.org/WRN/获取。<br>该rds文件包含以下数据集：<br>-<b>DRIVE</b>: 采用DEMETER2算法[2]处理得到的诺华DRIVE RNAi筛选基因依赖性评分[1]。<br>-<b>CRISPR</b>: 采用CERES算法[3]处理得到的Achilles CRISPR筛选基因依赖性评分。<br>-<b>GE</b>: 基因表达数据（log2(TPM)，仅包含蛋白编码基因）[4]。<br>-<b>CN</b>: Log2相对拷贝数数据[4]。<br>-<b>MUT_HOT</b>: 用于标记各基因在对应细胞系中是否存在热点错义突变的二元矩阵<br>-<b>MUT_DAM</b>: 用于标记各基因在对应细胞系中是否存在有害突变的二元矩阵<br>-<b>MUT_OTHER</b>: 用于标记各基因在对应细胞系中是否存在其他非同义突变的二元矩阵<br>-<b>MUT</b>: 包含DepMap 18Q4版本发布的全部突变调用信息的数据框[4]<br>-<b>RPPA</b>: 采用反相蛋白阵列技术得到的CCLE蛋白质丰度数据[4]。<br><b>参考文献</b><br>[1] McDonald, E.R. 等人. 《DRIVE计划：大规模深度RNAi筛选揭示的癌症依赖性与合成致死关系全集》. 细胞, 170, 577-592 (2017).<br>[2] McFarland, J.M. 等人. 《基于模型归一化与数据整合的大规模RNAi筛选癌症依赖性评估优化》. 自然·通讯, 9, 4610 (2018).<br>[3] Meyers, R.M. 等人. 《拷贝数效应的计算校正可提升癌症细胞CRISPR–Cas9必需性筛选的特异性》. 自然·遗传学, 49, 1779 (2017).<br>[4] 癌症细胞系百科全书联盟、癌症药物敏感性基因组学联盟. 《两类癌症细胞系数据集的药物基因组学一致性》. 自然, 528, 84–87 (2015).