1. Additional file 1 of Extru-seq: a method for predicting genome-wide Cas9 off-target sites with advantages of both cell-based and in vitro approaches
- Author
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Kwon, Jeonghun, Kim, Minyoung, Hwang, Woochang, Jo, Anna, Hwang, Gue-Ho, Jung, Minhee, Kim, Un Gi, Cui, Gang, Kim, Heonseok, Eom, Joon-Ho, Hur, Junho K., Lee, Junwon, Kim, Youngho, Kim, Jin-soo, Bae, Sangsu, and Lee, Jungjoon K.
- Abstract
Additional file 1: Fig. S1. Genome editing drugs and off-target prediction methods used in IND studies. Fig. S2. Optimization of Extru-seq conditions. Fig. S3. Extru-seq WGS data analyzed using IGV to reveal cleavage patterns. Fig. S4. Genome-wide off-target loci containing zero to six mismatches relative to the target. Fig. S5. Part of the GUIDE-seq results obtained from HEK293T cells. Fig. S6. Manhattan plot of Digenome-seq results obtained from HEK293T cells. Fig. S7. Manhattan plot of Extru-seq results obtained from HEK293T cells. Fig. S8. Box and whisker plots showing results from different off-target prediction methods for promiscuous sgRNAs targeting PSK9 and Albumin. Fig. S9. Indel ratios calculated following analysis of genomic DNA obtained from organs from C57BL/6 mice injected with two AAV8 vectors, respectively expressing Cas9 and sgRNA targeting either PCSK9 or Albumin. Fig. S10. Validation results from targeted deep sequencing of the top 10 predicted off-target sites. Fig. S11. GUIDE-seq results obtained from HeLa cells. Fig. S12. Manhattan plot of Extru-seq results obtained from HeLa cells. Fig. S13. Validation results from targeted deep sequencing of the top 10 predicted off-target sites. Fig. S14. Number of samples found in the intersections of Venn diagrams showing the overlap between off-target sites predicted by different methods. Fig. S15. Off-target sites, predicted by Extru-seq or GUIDE-seq and validated by deep sequencing. Fig. S16. Venn diagrams showing the number of predicted off-target sites. Fig. S17. The top 10 potential off-target loci predicted by Extru-seq for MSCs and HEK293T cells. Fig. S18. p-values obtained by the normalized rank sum test for each pair of off-target prediction methods [42–45].
- Published
- 2023
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