| URL: | https://pickles.hart-lab.org |
| Full name: | Pooled In-vitro CRISPR Knockout Library Essentiality Screens |
| Description: | The database of Pooled In vitro CRISPR Knockout Library Essentiality Screens.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. |
| Year founded: | 2018 |
| Last update: | 2022 |
| Version: | v3 |
| Accessibility: |
Accessible
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| Country/Region: | United States |
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| University/Institution: | University of Texas MD Anderson Cancer Center |
| Address: | Traver Hart Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA |
| City: | Houston |
| Province/State: | TX |
| Country/Region: | United States |
| Contact name (PI/Team): | Traver Hart |
| Contact email (PI/Helpdesk): | pickles@hart-lab.org |
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PICKLES v3: the updated database of pooled in vitro CRISPR knockout library essentiality screens. [PMID: 36350677]
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. |
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PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens. [PMID: 29077937]
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. |