Crispr Browser
This is a genome browser to visualize the results of CRISPR-dCas9 screens in bacteria. You can upload your own data or navigate through published datasets.
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Guide RNA design for CRISPRi in bacteria
Input the sequence of a target gene and this script will output candidate guide RNAs for the S. pyogenes dCas9 with predicted on-target activity and an analysis of off-targets. Predictions are made based on a model of dCas9's ability to block the RNA polymerase of E. coli (Calvo-Villamañán et al., 2020) .
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References
- Cui L, Vigouroux A, Rousset F, Varet H, Khanna V, Bikard D. A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9. Nature Communications 2018;9:1912.
- Rousset F, Cui L, Siouve E, Becavin C, Depardieu F, Bikard D. Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors. PLOS Genetics 2018;14:e1007749
- Calvo-Villamañán A, Ng JW, Planel R, Ménager H, Chen A, Cui L & Bikard D. On-target activity predictions enable improved CRISPR–dCas9 screens in bacteria. Nucleic Acids Res 2020