Extended Data Fig. 6: CBE, CBE-dCas9, and PE2 edited with HEK293_site_4.
a-b, Bar chart shows the C-to-T rates of all tested sites detected by Tracking-seq (a) and not detected by Tracking-seq (b). Cytosines upstream of the protospacer, cytosines within the protospacer, indels, and background cytosines are in blue, pink, purple, and grey, respectively. Background refers to cytosines located outside the protospacer but within ±50 bp from the 5′ end of the protospacer. Two technical replicates were performed for each site. Bars with one point and no error bar indicates PCR failures for one of the two replicates. Error bars indicate ± SD. c, The editing efficiency of CBE with dCas9 at the on-target site of HEK293_site_4, showing ~23% C to T conversion in the editing window. d, Tracking-seq signals at the on-target site. e, Comparison of the Track scores of CBE with nCas9 and CBE with dCas9. Each dot represents a candidate off-target site; the dashed line indicates the threshold for positive sites. f, Tracking-seq signals at a representative off-target site. g, Bar charts showing editing rates of off-target sites induced by PE2 detected by Tracking-seq. Dots in the bar charts indicate biological replicates. Precise editing refers to sequence changes that exactly match the reverse transcriptase template at the on-target site. All the other mutations fall into ‘undesirable substitution’ or ‘undesirable indel’. h, Sequences related to Off-2 with unusually high indel rates in g. The last four rows indicate representative sequences detected in the amplicon sequencing.
