Buganim, Y. et al. Cell 150, 1209–1222 (2012).

Studies of gene expression during cellular reprogramming to pluripotency typically examine populations of cells. But reprogramming is an inefficient and heterogeneous process: only a small fraction of cells are fully reprogrammed to stable induced pluripotent stem cells (iPSCs). Analysis of gene expression in single cells is likely to be required to fully understand the sequence of events during reprogramming. Using their previously established secondary mouse reprogramming system, Buganim et al. monitored expression of 48 genes (selected because they are involved in epigenetic regulation, cell cycle control and maintenance of the pluripotent state) in single cells at different stages of the reprogramming process. They identified transcripts that are predictive of the formation of stable iPSCs and thus propose earlier stochastic and later hierarchical phases of the reprogramming process.