High-throughput sequencing technics imposed themselves as a reference approach when it comes to analyze transcriptional modulation in different biological contexts. In this study, we investigated a certain amount of those modulations in Hydra. This work mainly focuses on transcriptional modulations induced by the effect of hydroxyurea (HU). This treatment synchronized most of the cells in S phase, before they pass to G2 phase. Therefore, study of differentially expressed genes at different time points during the treatment allowed us to produce a list of candidate genes regulated during cell cycle. Moreover, this sequencing allowed us to investigate possible cell reprograming of the remaining epithelial cells upon i- cell depletion due to the HU exposure. In this study, we also establish preliminary steps towards transcriptional modulation occurring during head regeneration of animals being decapitated or cut at a mid-gastric level. This approach allowed us to identify genes differentially expressed during this two kind of apical regeneration.