<p>Human-rated suborbital vehicles present the opportunity to conduct science during the transitions to space and back. This opportunity is enhanced by the ability to include researchers in the crew who can conduct real-time experiments in what is effectively a shirt-sleeve environment. While numerous suborbital flights have carried autonomous research payloads, suborbital vehicle systems have yet to be fully operationalized as platforms for scientists to physically conduct experiments. Therefore the present study was designed as an early step to advance this operationalization through a researcher-tended experiment on New Shepard flight NS-26, with the science objective to sample plant responses at four specific moments of the suborbital spaceflight experience – on the tower just before launch, after launch at capsule separation and entry into microgravity, just before reentry, and shortly after landing. The conduct of the experiment also further operationalized the use of Kennedy Space Center Fixation Tubes (KFTs) within suborbital flights by using duplicate KFTs to capture replicate samples preserved in RNAlater at each of the timepoints. Further, the replicated sampling during flight was precisely matched in real time with ground control sampling. This approach enabled a robust analysis of gene expression changes in Arabidopsis seedlings during the spaceflight experience. Rapid, specific reprogramming of the transcriptome occurred, especially during the boost and microgravity phases of the flight. Some of the differentially expressed genes were related to genes differentially regulated during longer-term orbital spaceflight; however, the nature of many of the metabolic pathways that were differentially regulated early in suborbital spaceflight suggests that entry into space produces a rapid, acute response involving misfolded proteins and other reactive oxygen species stresses—some of them involving mitochondrial processes.</p>