mRNA expression in iPS cells generated by a synthetic self-replicative RNA

We generated iPS cells with a synthetic self-replicative RNA that expresses four independent reprogramming factors (OCT4, KLF4, SOX2 and either c-MYC or GLIS1). We performed whole genome RNA sequencing (RNA-seq) of iPS cell clones, parental BJ and HUES9 ES cell controls. All iPS cell clones analyzed by RNA-seq showed unsupervised hierarchical clustering and expression signatures characteristic of human HUES9 ES cells that were highly divergent from parental human fibroblasts. RNA-seq in two OKS-iM iPS clones (generated from OCT4, KLF4, SOX2 and cMYC expressing RNA replicon), two OKS-iG clones (generated from OCT4, KLF4, SOX2 and GLIS1 expressing RNA replicon), HUES9 and BJ cells.