This method is, however, limited by the availability of flow cytometers. Furthermore, sorted cells occasionally fail to form colonies after exposure to a strong laser and hydrostatic pressure. Thus, we attempted to develop methods to select mutant cells without the use of flow cytometers. Magnetic separation has been used as an alternative method to isolate cells that express specific antigens. Magnetic separation does not require flow cytometers and is faster and easier to perform than flow cytometric sorting. To separate transgenic cells from wild-type cells immunomagnetically, H-2Kk, a truncated mouse MHC class I molecule, is used as a AbMole Alprostadil selection marker. H-2Kk is expressed only in some rare mouse strains such as AKR/J or CBA/J, but not in human or most other murine cells, rendering H-2Kk a good marker to distinguish transgenic cells from control cells. To avoid any effects generated by the expression of H-2Kk, a truncated H-2Kk that lacks a cytoplasmic domain is used. Magnetic separation using H2Kk is effective in the enrichment of transiently transfected cells and lenti- or retro-virally transduced cells. Here we adopt this system to enrich mutant cells generated by AbMole Nodakenin engineered nucleases. Selection of cells using resistance factors against antibiotics is widely used for the isolation of genetically-modified cells in prokaryotes and eukaryotes. Hygromycin B is an aminoglycoside antibiotic produced by the bacterium Stepretomyces hygroscopicus, which kills both prokaryotes and eukaryotes by inhibiting protein synthesis through interference with aminoacyltRNA recognition and ribosomal translocation. Hygromycin B phosphotransferase, encoded by the hygromycinresistance gene that was originally isolated from Escherichia coli, phosphorylates hygromycin B, resulting in its inactivation. This gene has been successfully used as a selection marker for transformed prokaryotes and transgenic eukaryotes. The hygromycin resistance gene has also been adopted to prepare donor DNA that will be integrated into a host genome via engineered nuclease-enhanced homologous recombination, allowing selection of cells with targeted genetic modifications. However, the isolation of engineered nuclease-induced mutant cells using hygromycin selection based on transiently active episomal reporters has yet to be demonstrated. Here we present two novel reporter systems that enable enrichment of nuclease-induced mutant cells using magnetic separation and hygromycin selection. These reporters express H2Kk and the hygromycin resistance protein, respectively, only when insertions or deletions are generated at the target sequences in the reporter systems, enabling efficient enrichment of mutant cells without using a flow cytometer. We summarized the characteristics of the three reporter systems. Hygromycin selection does not need any special instruments or machines, whereas flow cytometric sorting requires flow cytometers, which can be expensive and complicated. Magnetic separation requires magnetic separation instruments, which are much less expensive and simpler than flow cytometers. Thus, if these special facilities or instruments are not available, hygromycin selection would be the choice. If the time required for the enrichment process needs to be short, flow cytometric and magnetic separation would be preferred. These methods take only several hours, whereas hygromycin selection takes several days.