Migrating an existing application to the Cloud is a complex and multi-dimensional problem requiring in many cases adapting the application in significant ways. Looking specifically into the database layer of the application, i.e. the aspect providing data persistence and manipulation capabilities, this involves dealing with differences in the granularity of interactions, refactoring of the application to cope with remote data sources, and addressing data confidentiality concerns. Toward this goal, in this work we present an application migration methodology which incorporates these aspects, and a decision support, application refactoring and data migration tool that assists application developers in realizing this methodology. For purposes of evaluating our proposal we present the results of a case study conducted in the context of an eScience project.