Abstract: The present invention provides stably tagged stem cells and methods for producing stem cells comprising one or more tagged proteins using a gene editing system. The methods described herein enable the insertion of large fluorescent tags into a plurality of genomic loci to generate stem cells that are phenotypically and functional similar to the un-modified parent population. Stem cells produced by the methods described herein additionally retain the capacity to self-renew and differentiate into specialized cell types and can be used in assays and visualization of three-dimensional live cell imaging.