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.