Scripts and data associated with the analysis of whole-transcriptome gene expression profiles for two stony coral tissue loss disease (SCTLD) experiments: an ex situ transmission experiment conducted with Orbicella faveolata and Montastraea cavernosa corals and their associated algal symbionts (Durusdinium and Cladocopium, respectively), and an in situ antibiotic intervention experiment conducted with Montastraea cavernosa in southeast Florida