Reads from inner mantle of individual 29 from Logatchev
RNA from each mussel tissue was isolated using the RNeasy Mini Kit (Qiagen, Germany) in combination with QIAshredder homogenizers (Qiagen, Germany). Residual DNA contaminations were removed with the DNA free DNase Treatment & Removal Kit (Invitrogen/Ambion, Germany). After RNA quality and quantity checks on the Experion Automated Electrophoresis Station (Bio-Rad, Germany) samples were submitted to the Institute of Clinical Molecular Biology (Kiel, Germany) for multiplexed 2×101 bp paired-end RNA sequencing on an Illumina HiSeq2000 platform (Illumina, USA). Barcoded sequencing libraries were constructed with the TruSeq RNA Sample Preparation Kit v2, while cluster generation was performed with the TruSeq PE Cluster Kit v3-cBot-HS (Illumina, USA). RNA-Seq libraries for samples from Menez Gwen, Logatchev and Clueless were poly(A)-enriched and sequenced in an unstranded way. RNA-Seq libraries for samples from Lilliput were not poly(A)-enriched and three of them were sequenced in a strand-specific way (Lilliput 1?3 319-8). We multiplexed six unstranded libraries per Illumina lane, while the three stranded libraries were sequenced on a separate lane.