Additional file 1 of Expanding the CRISPR/Cas genome-editing scope in Xenopus tropicalis
Creators: name: Shi, Zhaoying
name: Jiang, Hao
name: Liu, Guanghui
name: Shi, Songyuan
name: Zhang, Xuan
name: Chen, Yonglong
Publisher: name: figshare
Year: 2022
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 1: Figure S1. DNA deep-sequencing data show the mutations induced by SaCas9 targeting the genes showed in Fig. 2a. For all the panels, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses show the percentage of this sequence in total sequencing reads. For target site designation, the gene name is in the middle, the prefix Sa- represents SaCas9. The suffixes -T1 and -T2 represent the first and the second target site designed in a given gene, respectively. Figure S2. DNA deep-sequencing data show the mutations induced by KKH SaCas9 targeting the genes showed in Fig. 2b. For all the panels, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses show the percentage of this sequence in total sequencing reads. For target site designation, the gene name is in the middle, the prefix KKH- represents KKH SaCas9. The suffixes -T1 and -T2 represent the first and the second target site designed in a given gene, respectively. Figure S3. T7EI assay data show the mutagenic activities of VQR Cas9, SpG Cas9, SpRY Cas9, and iSpyMac in X. tropicalis embryos. The targeting sites labelled in red, blue, and green are the effective ones for SpRY Cas9, SpG Cas9, and VQR Cas9, respectively. For target site designation, in addition to the gene name, the name of the Cas9 variant is used as a prefix and in some cases either the PAM motif or T1/T2 is indicated as a suffix. Figure S4. DNA deep-sequencing data show the mutations induced by VQR Cas9 targeting the genes showed in Fig. 3a. For all the panels, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses show the percentage of this sequence in total sequencing reads. Figure S5. DNA deep-sequencing data show the mutations induced by SpG Cas9 targeting the genes showed in Fig. 3a. For all the panels, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses show the percentage of this sequence in total sequencing reads. Figure S6. DNA deep-sequencing data show the mutations induced by SpRY Cas9 targeting the genes showed in Fig. 3a. For all the panels, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses show the percentage of this sequence in total sequencing reads. For target site designation, in addition to the gene name, the name of the Cas9 variant is used as a prefix and the PAM motif is indicated as a suffix. Figure S7. T7EI assay data show the mutagenic activities of xCas9 3.7 targeting non-NGG PAM sites in X. tropicalis embryos. The targeting sites labelled in red and blue are the effective ones with their effective gray values indicated at the bottom. The blue ones have been further verified by Sanger DNA sequencing. C, control. For target site designation, in addition to the gene name, the name of the Cas9 variant is used as a prefix and the PAM motif is indicated as a suffix. Figure S8. NGG xCas9 3.7 is ineffective in X. tropicalis embryos. a T7EI assay data show the mutagenic activities of xCas9 3.7 targeting NGG PAM sites in X. tropicalis embryos. The targeting sites labelled in red have been further verified by Sanger DNA sequencing shown in c. C, control. b Sanger DNA sequencing data show the mutations of bace2 induced by SpCas9. c The upper panel shows the Sanger DNA sequencing data of the bace2 mutation induced by xCas9 3.7 targeting exactly the same site shown in b. The lower panel shows the Sanger DNA sequencing data for xCas9 3.7-apc-163 site. For all the panels in b and c, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses represent the ratio of this sequence in the total colonies sequenced. Figure S9. Sanger DNA sequencing data show the mutations induced by SaCas9 and KKH SaCas9 targeting the genes showed in Fig. 5. For all the panels, the wild-type sequence is shown at the top with the target site highlighted in yellow and the PAM sequence in blue text. Red dashes indicate deletions and lowercase letters in red indicate insertions or mutations. The numbers in parentheses indicate ratio of this sequence in the total colonies sequenced. For target site designation, the gene name is in the middle, the prefixes Sa- and KKH- represent SaCas9 and KKH SaCas9, respectively. The suffixes -T1 and -T2 represent the first and the second target site designed in a given gene, respectively. Figure S10. T7EI assay data show no discernible mutagenic activities on potential off-target sites for LbCas12a, SaCas9, and KKH SaCas9 in X. tropicalis embryos. Potential off-target (OT) site is indicated as the last suffix. C, control.