Gilthead sea bream juveniles of Atlantic origin of 21-28 g body weight were acclimated during 42 days to a ramped oxygen concentration (3-4 ppm, 40-60% oxygen saturation according to LOS values). A third group of fish were pair-fed to the previously described group. Fish were recovered under normoxic conditions during a three week period.</p><p>These samples contain the raw read sequences of a skeletal muscle RNA-seq experiment performed after 42 days of hypoxic acclimation, before and after an exercise test until exhaustion in hypoxic conditions (4 ppm, 60% oxygen saturation) and after an exercise test until exhaustion performed after 3-week of normoxia recovery period.