Networks of enhancers and microRNAs drive variation in cell states

We measure gene expression changes in three naturally arising states of embryonic stem cells. These states exhibit intrinsic heterogeneity through varying at activity at subsets of enhancers. Variation at enhancers drives variation in protein coding genes and microRNAs, the latter of which further contribute to cell state variation across the population of ESC. Overall design: Examination of gene expression in three ESC states defined by Nanog and Sox2 levels in three replicates