CRISPR database

About the database

This database contains CRISPR targets for the mm10 genome. While some targets have been manually designed, most have been obtained from the automated whole-genome detection that we have introduced in our 2016 article.

If you use this database, please make sure to cite:
G. A. Sunagawa, K. Sumiyama, M. Ukai-Tadenuma, D. Perrin, H. Fujishima, H. Ukai, O. Nishimura, S. Shi, R. Ohno, R. Narumi, Y. Shimizu, D. Tone, K. L. Ode, S. Kuraku and H. R. Ueda (2016). "Mammalian reverse genetics without crossing reveals Nr3a as a short-sleeper gene". Cell Reports 14:1-16.

The article details the entire selection method. Candidates are first extracted from a gene's exons, based on their sequence, and then go through successive filtering steps. Candidates are eliminated if they appear multiple times in the genome, if their AT content is below 45%, if they contain TTTT, or if they are too close to the reverse primer for PCR amplification in the gRNA-template construction. They are also discarded if the corresponding gRNA has a poor secondary structure, or if the sequence has a high off-target risk. Candidates that pass all these steps are considered suitable targets, and are stored in a database.
This can be summarised by the following figure, reproduced from our artcile.

The database provides targets for 21,559 genes. For 19,536 genes, we have identified at least three targets. This means the triple-targeting method outlined in the article can be applied to 81.2% of the mm10 genome using this database.
Moreover, 71.9% of the gene has more than six independent targets, which corresponds to more than two sets of triple-target CRISPR gRNAs.