Fig. 2

Targeted large fragment deletion by bi-directional WT-PE (bi-WT-PE). a A diagram showing the design of bi-directional WT-PE for targeted deletion. A pair of pegRNAs were designed to target each side sequences (black) flanking the aimed fragment to be deleted (gray). The RT template of each pegRNA in class 1 bi-directional WT-PE (C1-WT-PE) is designed to contain aimed edit (in red) and a homologous arm (HA, in green) that is complementary to the PAM proximal end of the target region of the other pegRNA (right panel). And the RT template of pegRNA in class 2 bi-directional WT-PE (C2-WT-PE) is designed to contain only the edits but complementary with each other. b Agarose gel analysis of the amplicons of targeted deletions. A pair of primers flanking each target deletion were used to amplify the edited region. Bands with size match wild type or edited sequences were indicated. Parameters of pegRNA, including the length of edit and HA were indicated below the gel image. c Quantification of the targeted deletion by photoshop software analysis of the band intensity. d HTS analysis of the fragments containing aimed deletions. Three types of editing outcomes were observed in WT-PE mediated deletions and their relative ratios were quantified via HTS. Plots show mean ± s.d. of three independent biological replicates. e Diagram showing the design of a 16.8 Mbs deletion on the short arm of chromosome 11. f The presence of chromosome 11 with targeted deletions was detected by PCR analysis with primers indicated in Supplementary Table 4. Left panel showed the agarose gel image of the amplicons and right panel showed their Sanger sequencing chromatograms with residue spacer sequences marked with yellow and blue. g Quantifying the frequencies of targeted deletions by absolute quantitative PCR. The standard curves of wildtype- or edited-chromosome-specific fragment were shown in supplementary Fig. 8. Plots showed mean ± s.d. of three independent biological replicates