PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens

Lance C Novak; Juihsuan Chou; Medina Colic; Christopher A Bristow; Traver Hart

doi:10.1093/nar/gkac982

PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens

Nucleic Acids Res. 2023 Jan 6;51(D1):D1117-D1121. doi: 10.1093/nar/gkac982.

Authors

Lance C Novak¹, Juihsuan Chou^{2

3}, Medina Colic³, Christopher A Bristow¹, Traver Hart^{3

4}

Affiliations

¹ TRACTION, 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.
³ Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
⁴ Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Abstract

PICKLES (https://pickles.hart-lab.org) is an updated web interface to a freely available database of genome-scale CRISPR knockout fitness screens in human cell lines. Using a completely rewritten interface, researchers can explore gene knockout fitness phenotypes across cell lines and tissue types and compare fitness profiles with fitness, expression, or mutation profiles of other genes. The database has been updated to include data from three CRISPR libraries (Avana, Score, and TKOv3), and includes information from 1162 whole-genome screens probing the knockout fitness phenotype of 18 959 genes. Source code for the interface and the integrated database are available for download.

Publication types

Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural

MeSH terms

CRISPR-Cas Systems*
Cell Line
Clustered Regularly Interspaced Short Palindromic Repeats
Databases, Genetic*
Gene Knockout Techniques
Gene Library
Genome
Humans

Abstract

Publication types

MeSH terms

Grants and funding