HT29 reference dataset

We provide a dataset that can be used (through a dedicated R package and metrics) for the assessment of novel experimental pipelines upon the execution of a single calibration viability screen of the HT-29 human colon cancer cell line, with the experimental setting described in [1], employing a commercially available genome-wide library of single guide RNAs: the Human Improved Genome-wide Knockout CRISPR (Sanger) Library [2]. This dataset contains results from screening the HT-29 in multiple batches with the Sanger library, at multiple intermediate levels of preprocessing, and outcomes from several quality control tests on the resulting data. Data and accompanying R package can be used as a toolkit for benchmarking newly established experimental pipelines for CRISPR-Cas9 recessive screens, via the generation of a final quality-control report. The R package is available at https://github.com/DepMap-Analytics/HT29benchmark <br> References: [1] Behan FM, Iorio F, Picco G, et al. <em>Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens</em>. <strong>Nature</strong>. 2019 Apr;568(7753):511-516. doi: 10.1038/s41586-019-1103-9. Epub 2019 Apr 10. <br> [2] Tzelepis K, Koike-Yusa H, et al. <em>A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia</em>. <strong>Cell Rep</strong>. 2016 Oct 18;17(4):1193-1205. doi: 10.1016/j.celrep.2016.09.079.

本数据集可通过专用R包及配套指标，用于评估针对HT-29人结肠癌细胞系开展单次校准性存活筛选的新型实验流程；该实验设置参照文献[1]，采用商用化全基因组单向导RNA（single guide RNA）文库：人类优化全基因组成簇规律间隔短回文重复序列（CRISPR）（Sanger）敲除文库[2]。
本数据集包含使用该Sanger文库对HT-29细胞进行多批次筛选的结果，涵盖多个中间预处理阶段，同时包含对所得数据开展的多项质量控制测试结果。
本数据集及配套R包可作为工具集，用于通过生成最终质量控制报告，对新建的成簇规律间隔短回文重复序列相关蛋白9（CRISPR-Cas9）隐性筛选实验流程进行基准测试。
该R包可从以下地址获取：https://github.com/DepMap-Analytics/HT29benchmark
参考文献：
[1] Behan FM, Iorio F, Picco G, 等. *基于CRISPR-Cas9筛选的癌症治疗靶点优先级排序*. **自然**. 2019年4月;568(7753):511-516. doi: 10.1038/s41586-019-1103-9. 2019年4月10日在线发表.
[2] Tzelepis K, Koike-Yusa H, 等. *CRISPR敲除筛选识别急性髓系白血病的遗传脆弱性与治疗靶点*. **Cell Reports**. 2016年10月18日;17(4):1193-1205. doi: 10.1016/j.celrep.2016.09.079.