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The high heterogeneity of 5G use cases requires the extension of the traditional per-component testing procedures provided by certification organizations, in order to devise and incorporate methodologies that cover the testing requirements from vertical applications and services. In this paper, we introduce an experimentation methodology that is defined in the context of the 5GENESIS project, which aims at enabling both the testing of network components and validation of E2E KPIs. The most important contributions of this methodology are its modularity and flexibility, as well as the open-source software that was developed for its application, which enable lightweight adoption of the methodology in any 5G testbed. We also demonstrate how the methodology can be used, by executing and analyzing different experiments in a 5G Non-Standalone (NSA) deployment at the University of Malaga. The key findings of the paper are an initial 5G performance assessment and KPI analysis and the detection of under-performance issues at the application level. Those findings highlight the need for reliable testing and validation procedures towards a fair benchmarking of generic 5G services and applications.