CRISPR-Ca9 pooled drop out screen of 14 immortalized human cancer cell lines used to test CRISPRcleanR

We performed a genome-wide CRISPR-Cas9 loss-of-function screen on 14 immortalised human cancer cell lines that are a subset of the Genomics of Drug Sensitivity in Cancer (GDSC) panel [1]. These cell lines were transduced with a Cas9 lentiviral expression vector creating cells with stable expression of Cas9 endonuclease [2]. This was followed by transduction of a library of sgRNA (90,709 sgRNAs; targeting 18,000 genes, 5 targeting sgRNAs per gene) [2]. Next generation sequencing of the pool of sgRNAs at the beginning and at the end of the experiment produced the raw count files contained in this dataset. It is possible to identify sgRNAs targeting essential genes, via quantification of the corresponding fold changes between initial and final measurements (logFCs). The sgRNAs that have a significant reduced count over the course of the experiment were deemed to be depleted and as such, defined as having targeted an essential gene.

This data was generated to test the performances of the CRISPRcleanR method (https://github.com/francescojm/CRISPRcleanR) in unsupervised correcting gene independent cell responses to CRISPR-Cas9 targeting [4].

References:
[1] Iorio et al., A landscape of pharmacogenomic interactions in cancer. Cell 2016
[2] Tzelepis et al., A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia. Cell Reports 2016
[3] Iorio et al., Unsupervised correction of gene independent cell responses to CRISPR-Cas9 targeting, In preparation