In this study we performed a transcriptomic analysis of two tissues (gills and digestive gland) from wild cockles Cerastoderma edule sampled in Ria de Aveiro, Portugal, in two different seasons (with and without DTSs) of the year 2019. Preserved samples in RNAlater solution were transposed to 2 ml tubes pre-filled with ceramic beads (Precellys Ceramic kit 1,4) and then homogenized in homogenization buffer (RLT buffer) using an automatic bead-based homogenizer (Bertin Technologies, Montigny-le-Bretonneux, France) with a custom program (speed 5500 RPM at 0 C 2 x 20 sec cycles 30 sec pause). The supernatant containing a pool from the five biological replicates were recovered and conducted for total RNA extraction using Qiagen RNeasy Mini kit (Venlo, The Netherlands) according to the fabricant instructions. Total RNA concentration and RNA integrity of four samples corresponding to control samples (without toxins) gills (Gc), digestive glands (DGc), and contaminated samples (exposed or contaminated with shellfish toxins) gills (Ge) and digestive glands (DGe) were evaluated with the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA), prior the total RNA sequencing using illumina TruSeq Stranded Total RNA Library Construction with Ribo-Zero NovaSeq 6000.