An in situ experiment was conducted in Southeast Florida to assess transcriptomic responses prior to and two weeks following application of CoreRx Base 2B with amoxicillin on SCTLD-affected Montastraea cavernosa. A complementary ex situ disease challenge experiment was conducted to expose fragments of M. cavernosa and Orbicella faveolata to SCTLD-affected donor corals in order to compare transcriptomic profiles among clonal individuals from disease-unexposed, exposed/displaying disease signs, and exposed/not displaying disease signs treatment groups. This repository contains raw sequence files associated with both experiments, prepared using the Tag-Seq pipeline.