Generation and characterization of inducible KRAB-dCas9 iPSCs from primates for cross-species CRISPRi

Comparisons of molecular phenotypes across primates provide unique information to understand human biology and evolution and single-cell RNA-seq CRISPR interference screens are a powerful approach to analyze them. Here, we generate and validate three human, three gorilla and two cynomolgus iPS cell lines that carry a dox-inducible KRAB-dCas9 construct in the AAVS1 locus. We show that despite variable expression levels of KRAB-dCas9 among lines, comparable downregulation of target genes and comparable phenotypic effects are observed in a single-cell RNA-seq CRISPR interference screen. Hence, we provide valuable resources for performing and further extending CRISPRi screens in human and non-human primates. Overall design: Three human, three gorilla, and two cynolmolgus inducible KRAB-dCas9 iPS cell lines with an integrated SOX2-targeting gRNA were culture in +dox or -dox conditions for 4 days to compare between SOX2-knockdown (+dox) and normal condition (-dox).