Abstract: Objective To apply Padlock rolling-circle amplification (Padlock-RCA) for the analysis of in situ gene expression in individual cells during cell differentiation. Method Retinoic acid induced differentiation of mouse teratocarcinoma F9 model was used, Nanog mRNA expression in F9 cells before and after induced differentiation were analyzed with Padlock-RCA and compared with analysis using real time RT-PCR. Result Padlock-RCA can efficiently detect the level of Nanog mRNA expression in single cells . Nanog specific Padlock-RCA products were significantly decreased in F9 cell following retinoic acid induction, and confirmed with real time RT-PCR （P<0.05）. Conclusion We have successfully applied Padlock-RCA to analyze differential Nanog mRNA expressions before and after induced differentiation in single cells, and provided a reliable method for molecular and functional analyses of gene expression in single cell or cell subpopulations.

Key words: padlock probe, mouse teratocarcinoma cell, mRNA, differentiation