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Nucleic Acids Res. 2018 Jan 4;46(D1):D776-D780. doi: 10.1093/nar/gkx993.

PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens.

Author information

1
Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
2
UTHealth Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Abstract

The adaptation of CRISPR/Cas9 systems for pooled library genetic knockout screens in mammalian cells has substantially advanced the state of the art in human functional genomics. Screening panels of cell lines for genes whose knockout imposes a significant fitness defect has dramatically expanded our catalog of high-confidence essential genes, and has already proven useful in identifying tumor-specific essential genes for the development of targeted therapies. However, nonexperts currently lack an easy to use way to access this data and to identify whether their genes of interest are essential across different genetic backgrounds. The volume of screening data is expected to grow massively, making the problem more intractable. Here we describe PICKLES, the database of Pooled In vitro CRISPR Knockout Library Essentiality Screens, where end users can display and download raw or normalized essentiality profiles for more that 18 000 protein-coding genes across more than 50 cell lines. An additional data set with 15,000 genes targeted by pooled library shRNA in over 100 cell lines is also included. Researchers can see at a glance the relative fitness defect and tissue specificity of their genes of interest, generate and save figures locally, and download all raw data. The database is available at http://pickles.hart-lab.org.

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