Purpose: This RNA-Seq study aims on elucidate the major trends in the transcriptional profile of soybean embryonic axes during germination. Methods: Soybean seeds were germinated in soaked cotton at 28ÂºC. In addition to dry seeds, seeds were harvested at 3, 6, 12, 24 hours after imbibition. Then the embryonic axes were separated from the cotyledons for RNA extraction. For each biological sample, 20 seeds were used. Results: Identification of genes and pathways involved in metabolism, hormone signaling and transcriptional regulation. Overall design: Large-scale analysis of soybean embryonic axis in five time points during germination: dry, 3, 6, 12 and 24 hours after imbibition.