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This study was designed to identify changes in gene transcription that occur in the soleus muscle of untrained, 10-wk-old rats after a single aerobic exercise bout, and to identify which families of genes are most likely affected.Rats were either run for 2 h and killed 1 h after exercise, or they remained sedentary and were killed at a matched time. Soleus muscles from each animal were examined using DNA microarrays, four genes related to RONS were analyzed by PCR, and two proteins were checked by Western blot analysis.The microarray identified 52 genes significantly altered by the exercise. The major gene families altered were metabolism, apoptosis, muscle contraction, transcription/cell signaling, tissue generation, and inflammation. Real-time PCR was performed on four genes (NFκB, TNFα, Atf3, and Mgst1), and the results from PCR analysis agreed with the microarray results. NFκB and TNFα were unaltered, whereas Atf3 was upregulated and Mgst1 was downregulated in the exercised soleus muscles. NFκB protein level was not different between the two groups, whereas Atf3 protein level was elevated in the exercise group according to Western blot analysis.These data suggest that 1 h after a 2-h run at approximately 65% of V˙O2max, the soleus muscle undergoes significant gene-transcript changes. Also, the genes examined with the real-time PCR matched the microarray results and the measured protein concentration concentrations agreed with gene-transcript data at the 1-h postexercise time point.