DepMap 19Q4 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 689 cell lines, the RNAseq data includes 1249 cell lines, and the copy number data includes 1682 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
CCLE_fusions.csv and CCLE_fusions_unfiltered.csv were swapped in v1, they are correct now.

## 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.

本数据集为布罗德研究所（Broad Institute）癌症依赖性图谱（Cancer Dependency Map, 简称DepMap）项目的组成部分，涵盖癌症细胞系的多组学数据：包括以Achilles为前缀的Avana文库CRISPR-Cas9全基因组规模敲除结果，以及以CCLE为前缀的突变、拷贝数与基因表达数据。本次我们对文件集进行了重新打包，纳入了DepMap产出的全部季度更新数据集。

当前Avana文库CRISPR-Cas9全基因组规模敲除数据已扩展至覆盖689株细胞系，RNA测序（RNA-seq）数据覆盖1249株细胞系，拷贝数数据则覆盖1682株细胞系。有关数据处理流程的更新细节，请参阅README文件。

随着筛选工作的持续推进，我们将按季度发布更多癌症依赖性数据，供无限制使用。若需获取最新可用数据集、开展进一步分析或订阅邮件列表，请访问https://depmap.org。

实验方法与CERES算法的详细描述已发表于http://dx.doi.org/10.1038/ng.3984。部分细胞系的拷贝数数据基于桑格研究所（Sanger Institute）的全外显子组测序数据（COSMIC: http://cancer.sanger.ac.uk.cell_lines，欧洲基因组-表型组档案（EGA）登录号：EGAD00001001039），并通过CCLE流程重新处理完成。有关CCLE基因表达流程及工具版本的详细说明，可访问https://github.com/broadinstitute/gtex-pipeline/blob/v9/TOPMed_RNAseq_pipeline.md查看。

## V2版本更新说明
在V1版本中，CCLE_fusions.csv与CCLE_fusions_unfiltered.csv存在文件互换错误，当前版本已完成修正。

## V3版本更新说明
由于细胞系指纹分型（身份验证）出现问题，UACC62_SKIN_CJ1_RESISTANT细胞系已从Public 19Q4版本的Achilles文件中移除。该细胞系的数值已在以下文件中被设为缺失值（NA）：Achilles_gene_effect.csv、Achilles_gene_effect_unscaled.csv、Achilles_gene_dependency.csv、Achilles_logfold_change.csv、Achilles_raw_readcounts.csv。