Extended Data Fig. 2: PAM compatibilities of small Cas9s in human cells.
a, Heatmaps showing the average indel frequencies in the target sequences with the indicated PAM sequences. Indel frequencies were measured four days after transduction of the paired libraries in SaCas9-, SaCas9-KKH-, eSaCas9-, and efSaCas9-expressing cells; in the cells expressing the other three small Cas9s, indel frequencies were measured seven days after transduction. Protospacers for which the highest indel frequencies were < 5% across candidate PAM sequences were excluded from the analyses. Fixed positions and nucleotides are indicated above each heatmap. For instance, to evaluate the preferences for the 3rd, 4th, and 5th nucleotides of the PAM for SaCas9, the 6th and 7th nucleotides of the PAM were fixed as TN. The numbers of analyzed protospacers (n) are as follows: SaCas9, n = 29; SaCas9-KKH, n = 29; eSaCas9, n = 29; efSaCas9, n = 29; SaCas9-HF, n = 29; SaCas9-KKH-HF, n = 29; St1Cas9, n = 27. b, Summary of the analyzed PAM compatibilities.
