title: RNA-seq of the mantle from group 1 - sample 2
design: For each collected oyster, total RNA was extracted from mantle using the RNeasy Blood and Tissue Kit (Qiagen), following the manufacturer's instructions. RNA concentration and purity were measured using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific), considering 260/280 OD rations > 1.8 and OD 260/230  OD ratio > 1.8. A Qubit Fluorometer (Invitrogen, Waltham, MA, USA)  was also used  to measure RNA concentration.  RNA integrity was assessed by denaturing agarose gel electrophoresis with formaldehyde. The total RNA from the samples was purified for transcriptome analysis using the commercial TruSeq Stranded mRNA Kit (Illumina, San Diego, CA, USA), according to the manufacturers instructions. RNA quality and quantity were measured using NanoPhotometer spectrophotometer, Qubit RNA Assay Kit in Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA), and TapeStation (Agilent Technologies, Santa Clara, CA, USA). The Illumina NextSeq platform was used to generate 75bp paired-end reads.