mbiodinium density was relatively constant throughout the course of the experiment, in the range of 1.31.6 algal cells 106 cm2. By day 29, after 8 days of exposure to water at 31uC, both coral nubbins that had not been exposed to thermal pre-conditioning and those exposed to pulse treatments had suffered significant bleaching, Symbiodinium densities having decreased.70%. By contrast, no significant declines in symbiont density were observed at that time in corals that had been subjected to sustained preconditioning treatments . Comparison of Gene Expression Levels Our intent in applying microarray analyses was to shed light on the transcriptional differences between thermal tolerance and thermal injury. To investigate changes in gene expression associated with thermal tolerance, microarrays were used in a three way comparison between preconditioned, non-order ONX-0914 preconditioned and control coral nubbins. Secondly, we explored changes in gene expression associated with thermal injury by comparing NPC and control corals. Note in reference to gene expression results, the terms preconditioned, PC, and S1 Coral Thermal Tolerance 3 Coral Thermal Tolerance collectively refer to the 10-day preconditioning treatment. The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE41435. Our microarray analyses detected no differentially expressed genes between treatments on Day 4 or Day 20. ANOVA and pairwise comparisons of the microarray data identified differentially expressed genes after two, four, and eight days of thermal challenge. The microarrays contained numerous redundant features, with many ESTs forming single contigs. All redundancies in our dataset were congruent, with gene expression trends in agreement. At two days of 31uC thermal challenge, 23 genes were differentially 
expressed between non-preconditioned corals and control corals, while six genes were differentially upregulated in S1 compared to controls. At this sampling point, no differences between non-preconditioned and preconditioned treatments were detected by our analyses. Still prior to visual signs of thermal bleaching and detectable symbiont loss, at four days of 31uC thermal challenge 27 genes were differentially expressed between non-preconditioned corals and control corals, 32 genes showed differences in preconditioned compared to controls, and one gene was downregulated between preconditioned and non-preconditioned treatments. With eight days of thermal challenge at 31uC the nonpreconditioned corals are exhibiting substantial bleaching, with the loss of nearly 80% of Symbiodinium. At this point, 70 genes were differentially expressed in comparisons of nonpreconditioned to control corals, 42 differentially expressed between preconditioned and control, and nine genes identified in the comparison of preconditioned to non-preconditioned treatments . in the number of genes expressed, as well as the magnitude of expression. After four days at 31uC, 74% of differentially expressed genes are shared between S1/Control and NPC/ Control. The number of genes shared between NPC/C and PC/C continues to increases with time, with still more, 34 genes, shared after eight days of thermal challenge. In all cases of shared, differentially expressed genes between NPC/Control and S1/control, the NPC/Control comparison has higher magnitude gene expression. The majority of shared genes differ by more than one-fol