GSM7843757: UpT-185-02, rnaseq; Acropora palmata; RNA-Seq
Total RNA was extracted from the same 32 A. palmata fragments used in WGBS as previously noted. The tissue from each fragment was homogenized in TRIzol reagent (Ambion, Life Technology) before centrifugation with chloroform for 15 minutes at 12,000 x g at 4 ºC. The aqueous phase was then isolated and cleaned using Qiagen RNeasy Mini kit (Qiagen), as per the manufacturer's protocol with an additional on-column DNase treatment using RNase-Free DNase Set (Qiagen). Total RNA was sent to Admera Health (New Jersey, USA) where concentration and purity was re-analyzed (Qubit® dsDNA BR Assay Kit on a Qubit® 2.0. Fluorometer).  5 of these samples failed sequencing and were not included in the final transcriptomic analysis RNA libraries for 2x150bp paired-end sequencing were prepared using the NEBNext Ultra II Nondirectional Library Prep Kit with polyA selection (New England Biolabs, Inc.). Samples were run on one plate of the Illumina NovaSeq platform. Illumina universal adapters and reads below PHRED of 22 were trimmed using Cutadapt62. Filtered reads were aligned to the Acropora palmata genome assembled by Sheila Kitchen 2023; unpublished using the program STAR, and read counts compiled into a .tab file