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To identify potential biomarkers of salt stress in the freshwater mussel Elliptio complanata, we examined transcriptional responses of the common mussel Elliptio complanata to controlled NaCl exposures. The data set is a table of counts, with the rows being the transcripts detected in the samples in the experiment and the columns identifying the samples. Four mussles were exposed to normal freshwater and four mussels were exposed to high salinity (two ppt), for a period of seven days.