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

References:

[1] Behan FM, Iorio F, Picco G, et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature. 2019 Apr;568(7753):511-516. doi: 10.1038/s41586-019-1103-9. Epub 2019 Apr 10.

[2] Tzelepis K, Koike-Yusa H, et al. A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia. Cell Rep. 2016 Oct 18;17(4):1193-1205. doi: 10.1016/j.celrep.2016.09.079.

本数据集可搭配专用R包与配套评估指标，用于对基于HT-29人结肠癌细胞系的单轮校准性存活筛选实验所涉及的新型实验流程开展评估。实验设置详见参考文献[1]，所用试剂为商用全基因组单向导RNA（single guide RNA）文库——人类优化型全基因组CRISPR敲除（Sanger）文库[2]。
本数据集包含多批次使用该Sanger文库筛选HT-29细胞的实验结果，覆盖多个预处理中间阶段的数据，以及针对所得数据开展的多项质量控制测试结果。
依托本数据集与配套R包，研究人员可通过生成最终质量控制报告，对新建的CRISPR-Cas9隐性筛选实验流程开展基准测试。
该配套R包可从以下公开地址获取：https://github.com/DepMap-Analytics/HT29benchmark

参考文献：
[1] Behan FM, Iorio F, Picco G 等. 利用CRISPR-Cas9筛选优先确定癌症治疗靶点. 《自然》. 2019年4月;568(7753):511-516. DOI: 10.1038/s41586-019-1103-9. 2019年4月10日在线出版.
[2] Tzelepis K, Koike-Yusa H 等. CRISPR缺失筛选鉴定急性髓系白血病的遗传脆弱性与治疗靶点. 《细胞报告》. 2016年10月18日;17(4):1193-1205. DOI: 10.1016/j.celrep.2016.09.079.