Extended Data Fig. 1: Target sequence preferences and PAM compatibilities of Cas9 in vitro and in cultured cells. | Nature Biomedical Engineering

Extended Data Fig. 1: Target sequence preferences and PAM compatibilities of Cas9 in vitro and in cultured cells.

From: High-throughput evaluation of in vitro CRISPR activities enables optimized large-scale multiplex enrichment of rare variants

Extended Data Fig. 1

a, Sequence preferences at each position in targets that are cleaved efficiently (top 20%) compared to inefficiently (bottom 20%) with matched sgRNAs, in vitro and in cultured cells (HEK239T, HeLa, Hepa 1-6, and B16-F10). The y-axis represents the log2 odds ratio of nucleotide frequencies between efficiently and inefficiently cleaved target sequences. A positive log odds ratio indicates a preference for the nucleotide in efficiently cleaved targets at that position, whereas a negative value signifies a preference for the nucleotide in inefficiently cleaved targets at the respective position. The number of target sequences (n) = 33,309 in vitro and 33,309 in HEK293T, 354 in HeLa, 352 in Hepa 1-6, and 348 in B16-F10 cells. b, Heat maps showing the average SpCas9-induced cleavage indices in vitro (left) and the average indel frequencies in HEK293T cells (right) for each 4-nt PAM sequence. The number of sgRNA and target sequence pairs per 4-nt PAM sequence (n) = 27 (in vitro) and 30 (HEK293T).

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