Additional file 1 of Evaluation of CRISPR gene-editing tools in zebrafish

Additional file 1: Supplementary Figure 1. Editing efficiencies across 50 gRNAs with different GC content. Supplementary Figure 2. Mosaicism predicted using Illumina sequencing of G0 mutant larvae. Supplementary Figure 3. Network analyses of the shared differentially expressed genes in Cas9 enzyme and Cas9 mRNA injected larvae. Supplementary Table 1. Oligonucleotides utilized for all assays performed throughout the project. Supplementary Table 2. On-target efficiency scores for the 50 gRNAs obtained from different in silico prediction tools, empirical cleavage scores in vivo using Sanger sequencing and sequence deconvolution tools (TIDE and ICE), from the in vitro assay CIRCLE-seq (RPMN), and Illumina sequencing using the CrispRVariants software. Supplementary Table 3. Description of the off-targets predicted by CRISPRScan and CIRCLE-seq for the 50 evaluated gRNAs. The percentage of sites intersecting genes from the CRISPRScan tool was obtained from the top 30 predicted off-targets since the tool only provides detailed information from these. Supplementary Table 4. List of the frameshift variants identified in protein-coding genes in samples injected with either Cas9 enzyme or Cas9 mRNA using uninjected batch-siblings as reference. Supplementary Table 5. Illumina mosaicism percentages observed in larvae injected with Cas9 (enzyme or mRNA), catalytically dead Cas9 (dCas9), scrambled gRNA, uninjected batch siblings, and a finclip from their crossing parents. Supplementary Table 6. List of DE genes observed in Cas9-injected samples relative to uninjected batch-siblings and siblings from another batch. Supplementary Table 7. List of gene ontology terms enriched in upregulated genes found in both injection treatments (Cas9 enzyme and Cas9 mRNA).