Methods and compositions for selecting ES cells that are germline competent are provided, including gene expression arrays of from one to about 300 or more genes. Selecting ES cells that are competent for germline transmission by comparing the expression of one or more genes between an ES cell that is competent at germline transmission with an ES cell of interest is described. Selecting ES cells likely to be competent at germline transmission, based on their level of expression of gtl2, is also described.
