Single Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media

We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlexTM and TeSRTM-E8TM media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine-learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single cell RNA sequencing analysis of iPSC lines grown in both media is the first report of the molecular signature of StemFlex medium and how it compares to that observed in TeSR-E8 medium.