Prediction of gRNA efficiency by CRISPR-kp, position-specific mononucleotide feature-based scoring. (A−F) Performance of CRISPR-kp on independent crRNA efficiency data in comparison with CRISPRscan and Rule Set 2. CRISPR-kp scores were obtained by summing the respective mononucleotide feature [−log10(P-value)] values, in which negative values were given for disfavored mononucleotide features (Supplementary Table S8). Cleavage efficiencies of the second set of 27 crRNAs were determined using the dgRNA RNP complex assembled with WT or HiFi Cas9 with ICE (Supplementary Figure S4). Indel frequencies (in %) obtained with WT Cas9 (A−C) and HiFi Cas9 (D−F) were compared to scores obtained with CRISPR-kp (A,D), CRISPRscan (B,E) and Rule Set 2 (Doench/Fusi 2016) (C, F) by scatter plots. (G−I) Performance of CRISPR-kp on published data in comparison with CRISPRscan and Rule Set 2. Reported gRNA efficiencies assessed with RNP injections into zebrafish embryos (9,24,54,55) are compared with their CRISPR-kp (G), CRISPRscan (H), and Rule Set 2 (Doench/Fusi 2016) (I) scores. gRNA sequences and their CRISPR-kp scores are shown in Supplementary Table S8. Spearman correlation coefficients (rs) are indicated in each panel. In panels G-I, Spearman correlation coefficients for data including Hoshijima's dgRNAs are shown in parentheses.
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