RNA-Seq of Loripes lucinalis Individual T_D gill endosymbiont from Elba, Italy
DNA and RNA were co-extracted from one whole gill of five Loripes lucinalis individuals (not the same five individuals as used for genome sequencing) according to the manufacturerŐs instructions using an AllPrep DNA/RNA mini kit (Qiagen). From each sample, at least 10 ng RNA were used for paired-end library preparations. Total RNA was converted to double stranded cDNA and amplified linear with the Ovation RNA-Seq System V2 kit (NuGEN). Then 300 ng double-stranded cDNA was fragmented to an average size of 400 bp (Covaris). Illumina-compatible libraries were generated with the NEBNext¨ UltraŞ DNA Library Prep Kit for Illumina¨ kit (NEB). Finally, fragments were enriched by a PCR step for six cycles. Quality assessment was done at various steps at the RNA or DNA level with an Agilent Bioanalyser (Agilent). DNA was quantified by fluorometry (Qubit, Thermo Fisher Scientific, Waltham, MA). Libraries were quantified by fluorometry, immobilized and processed onto a flow cell with a cBot (Illumina) followed by sequencing with TruSeq v3 chemistry on a HiSeq2500 at the Max Planck Genome Centre in Cologne, Germany. For each individual, 26 million Illumina HiSeq 2_100 bp paired-end reads were sequenced.