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Genome editing of stem cells can be done quickly and efficiently, with the right tools. Presented here is a streamlined, robust experimental protocol to genetically engineer both gene knock-in and gene knockout in induced pluripotent stem cells (iPSCs). We describe a step-by-step protocol for easily engineering genetic changes in stem cells with targeting efficiencies between 55-85%. These high efficiencies can be achieved with this protocol through optimization of several key parameters including media conditions, guide RNA (gRNA) design, Cas9 format, Cas9:gRNA concentration ratios, and transfection conditions for CRISPR-Cas9 delivery.