Strain differences during early iPSC reprograming. Gross strain differences in efficiency to generate induced pluripotent stem cell (iPSC) colonies were observed after 8 days of mouse embryonic fibroblast (MEF) reprograming as visualized in these photographs with alkaline phosphatase (AP) staining (A). Strain differences were quantified by total number of colonies (B), percentage of colonies positive for alkaline phosphatase staining (C) and percentage of cells positive for SSEA-1 (D). NON/LtJ and CAST/EiJ strains were consistently more efficient than other strains in generating early iPSCs. These differences were not believed to be due to strain differences in MEF transducibility, as demonstrated by the percentage of cells positive for green fluorescent protein (GFP) on day 8 following transduction with a lentiviral GFP vector (E). Experiments were performed using MEFs derived from 2 different embryos for each strain (data presented as mean ± SD).