Open Access This project studied the effects of thermal stress on gene expression in the Staghorn coral (Acropora cervicornis). At four seasonal time points, tissue from at least ten colonies at three nurseries were exposed to three temperature treatments for one hour then preserved in RNALater. RNA was extracted with TRI Reagent then cleaned with a Qiagen RNEasy kit. A subset of samples were chosen and pooled for RNA-Seq. The subset included genotypes from 2 of the 3 nurseries (Upper Keys and Lower Keys), 2 of the 4 seasonal collections (Summer 1 and Winter 1), and all 3 temperature treatments (ambient, hot, and cold), resulting in 12 libraries. For each library, RNA from 7 of the 10+ genotypes at each nursery were pooled (84 samples total). Following the manufacturer’s protocol, 150 bp single reads were generated from oligo(dT)-selected total RNA using the Illumina TruSeq Stranded mRNA HT Kit. mRNA sequencing libraries were individually barcoded, multiplexed in equal quantities, and run on three lanes of the Illumina HiSeq 2000 platform. The data were demultiplexed into 12 individual library files.