Somatic embryogenesis is the process, in which differentiated somatic cells dedifferentiate and form an embryo. We characterized the initiation of somatic embryos (SEs) in the shoot apices of young seedlings of Arabidopsis thaliana. In this system, SEs are induced by application of osmotic stress and subsequent culture on media containing 2,4-dichlorophenoxyacetate (2,4-D). By using RNA-sequencing, we examined the transcriptome profiles of explants before and after stress application (named Shoot apex and Stress, respectively), and SE-forming and non-SE-forming explants at days 3 and 5 of SE induction, sorted by the presence or absence of the signal of an embryonic reporter (named day-3-positive, day-3-negative, day-5-positive, and day-5-negative-explants, respectively).