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. Author manuscript; available in PMC: 2016 Apr 1.
Published in final edited form as: Nat Methods. 2015 Aug 31;12(10):982–988. doi: 10.1038/nmeth.3543

Figure 4. Extending the CRISPR target repertoire with truncated, extended and 5′ mismatch-containing sgRNAs.

Figure 4

a. Boxplot representing the ranked normalized activity of each class of alternative sgRNAs, ordered by median activity. Shorter sgRNAs (GG16 and GG17) and sgRNAs inducing 1 mismatch in the 5′ GG (gG18 and Gg18) are the most active alternatives to the canonical GG18 sgRNA.

b. Biplot of sgRNA levels (log2 RPM) comparing 0 and 1.25 hpf, colored to indicate the frequencies of A and G in each sgRNA. Corresponding Spearman correlations between nucleotide frequencies and sgRNA stability (ratio of 1.25 hpf to 0 hpf levels) are shown (right), with p values indicated.

c. Biplot illustrating stable and unstable groups of sgRNAs, defined by >2-fold enrichment or depletion between 0 and 1.25 hpf (log2 RPM) (left). sgRNAs with low read-counts (bottom 10%) were excluded (grey lines). Box and whisker plots showing sgRNA activity (middle) and the input levels (right) in the stable and unstable sgRNAs. Mann-Whitney U test (**** p< 0.0001, ns: not significant).