This repository provides data and scripts used for the creation of the manuscript: "Multi-omic characterization of mechanisms contributing to rapid phenotypic plasticity in the coral Acropora cervicornis under divergent environments" Abstract Phenotypic plasticity is defined as a property of individual genotypes to produce different phenotypes when exposed to different environmental conditions. This ability may be expressed at behavioral, biochemical, physiological, and/or developmental levels, exerting direct influence over species' demographic performance. In reef-building corals, a group critically threatened by global change in the Anthropocene, non-genetic mechanisms (i.e., epigenetic and microbiome variation) have been shown to participate in plastic physiological responses to environmental change. Yet, the precise way in which these mechanisms interact, contribute to such responses, and their adaptive potential is still obscure. The present work aims to fill this gap by using a multi-omics approach targeting the complexity and interconnection among the components modulating phenotypic plasticity in staghorn coral (Acropora cervicornis) clones subject to different depth conditions. Results show conspicuous variation in lipidome, epigenome and transcriptome, but not in symbiotic and microbial communities. In addition, a potential shift towards a more heterotrophic feeding behavior was found in corals at higher depth. These observations are consistent with a multi-mechanism modulation of rapid acclimation in corals, underscoring the complexity of this process and the importance of a multifactorial approach to inform potential intervention to enhance coral adaptive capacity. Full Changelog: https://github.com/jarcasariego/ACER_clonal_divergence/commits/v.1.0