Flower development is a dynamics process in which floral organs are produced from pools of stem cells residing in meristems (Smyth et al., 1990). In order to obtain a high resolution map of the changes of gene expression during this process thus to provide insights into specific expression patterns and their underlying gene regulatory networks, an inducible system which allows us to obtain synchronized flowers (Wellmer et al., 2006) was used to collect stage-specific floral tissues at four stages (stages 0, 2, 4 and 8) for transcriptome profiling by RNA-seq . These stages represent the status of inflorescence meristem, floral meristem specification, floral organ specification and floral organ differentiation, respectively during Arabidopsis flower development. Overall design: We used the AP1-GR system to conduct RNA-seq experiments at different stages of flower development. Samples were generated from tissue in which the AP1-GR protein was induced using a treatment of 1 uM DEX to the shoot apex. The material was collect before treatment and 2, 4 and 8 days after treatment. Experiments were done in two or three biological replicates.