title: Ahemp_genome
design: RNA was isolated from the same colony that was used for genome sequencing. In addition, to  increase the diversity of expressed transcripts, we extracted RNA from two Acropora hemprichii nubbins of a different colony exposed to either low (33C) or high (36C) heat stress (3h ramp-up to heat stress, 3h heat-hold at respective heat stress target temperatures) using the Coral Bleaching Automated Stress System (CBASS) (Evensen et al. 2023; Voolstra et al. 2020). Nubbins were collected after an overnight recovery (11 h) phase in the dark. Upon collection, fragments were flash-frozen in liquid nitrogen and stored at -80C. For all RNA extractions, frozen A. hemprichii nubbins were placed in a sterile bag and the coral tissue was air blasted off the skeleton into 1 mL sterile artificial seawater. The resulting slurries were homogenized using a tissue homogenizer. A total of 200 L of the homogenate were mixed with 200 L RNeasy lysis buffer (Qiagen), snap-frozen in liquid nitrogen, and stored at -80C. Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturers protocol. RNA quality was assessed on a Bioanalyzer (Agilent Technologies). Libraries for all three samples were prepared from ~1 g total RNA using the TruSeq Stranded mRNA kit (Illumina, San Diego, CA, USA) following manufacturers instructions. The SuperScript II Reverse Transcriptase kit was used for the cDNA synthesis step and Agencourt AMPure XP beads for cleanup steps according to the manufacturer guidelines. Final libraries (average insert size ~200 bp) were quality-checked on a 2100 Bioanalyzer using the High Sensitivity DNA assay  and sequenced in paired-end mode (2 x 150 bp) on a HiSeq4000 at the KAUST BCL.