DepMap 20Q1 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 739 cell lines, the RNAseq data includes 1270 cell lines, and the copy number data includes 1713 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 sample_info.csv file in version 1 was missing lineage information for some cell lines. Version 2 corrects this.v3 changes: UACC62_SKIN_CJ1_RESISTANT has been removed from Public 19Q4 Achilles files due to an issue with fingerprinting. Values for this cell line have been NAed in the following files: Achilles_gene_effect.csv, Achilles_gene_effect_unscaled.csv, Achilles_gene_dependency.csv, Achilles_logfold_change.csv, Achilles_raw_readcounts.csv.

本数据集汇聚了Avana库CRISPR-Cas9基因组规模敲除实验（以Achilles为前缀）以及针对癌细胞系进行的突变、拷贝数和基因表达数据（以CCLE为前缀），这些数据构成了Broad研究所癌症依赖性图谱项目的一部分。我们对文件集进行了重新封装，以包含DepMap产生的所有季度更新数据集。Avana CRISPR-Cas9基因组规模敲除数据已扩展至涵盖739个细胞系，RNA测序数据包括1270个细胞系，拷贝数数据包括1713个细胞系。具体的数据处理流程和程序更新详情请参阅README文件。随着筛选工作的持续进行，我们将按季度发布更多未受限制使用的癌症依赖性数据。欲获取最新数据集、进一步的分析以及订阅我们的通讯列表，请访问https://depmap.org。实验方法和CERES算法的描述已发表在http://dx.doi.org/10.1038/ng.3984。部分细胞系基于Sanger研究所全外显子测序数据（COSMIC：http://cancer.sanger.ac.uk.cell_lines，EGA访问号：EGAD00001001039）经CCLE流程重新处理。CCLE表达流程的详细描述和工具版本可在此处找到：https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md.v2。版本更新如下：版本1中的sample_info.csv文件缺少某些细胞系的谱系信息，版本2进行了修正。版本3中，由于指纹识别问题，UACC62_SKIN_CJ1_RESISTANT已被从Public 19Q4 Achilles文件中移除，相关细胞系的值在以下文件中标记为NA：Achilles_gene_effect.csv、Achilles_gene_effect_unscaled.csv、Achilles_gene_dependency.csv、Achilles_logfold_change.csv、Achilles_raw_readcounts.csv。