Genetic manipulation is a vital tool utilized to understand the molecular mechanisms that regulate biological processes. Site specific genetic manipulations could be carried out in mouse embryonic stem cells (ESCs) due toa higher efficiency of homologous recombination frequency inthese cells. However, these manipulations are generallyinefficient. The site-specificnucleases like TALENs and CRISPRs have made the process of engineering the genomes easier and more efficient in ESCs.The genome editing tools have enabled the genetic manipulation of the somatic cell lines which was earlier practically impossible. I will be discussing some of the genome engineering strategies developed and utilized in our lab to engineer the genome of stem cells and mice. I will also discuss how the CRISPR based genome editing has enabled us to generate multiple types of modifications like loss of function, gain of function, fluorescent protein reporter stem cell lines to address some of the questions pertaining to understanding the stem cell state transition and early embryonic development in mice.