This study was conducted to uncover the underlying molecular mechanisms by which microgravity impacts cell wall architecture in the model plant Arabidopsis thaliana using the Vegetable Production System (Veggie) housed on the International Space Station (ISS). Based on our previous space flight studies using the Biological Research in Canisters (BRIC) hardware on the STS-131 Space Shuttle mission, we found that plants respond to microgravity in large part through the transcriptional reprogramming of genes that control cell wall remodeling. This follow-up spaceflight experiment called the Advanced Plant EXperiments (APEX 03-1) in Space was designed to use Veggie unit on the ISS and on the ground unit on the Space Station Processing Facility (SSPF) to probe deeper into spaceflight-induced cell wall associated transcript expression changes. In this study we used RNA-Seq in combination with glycome profiling (glycomics) to correlate spaceflight-induced gene expression changes with actual cell wall modifications within seedlings.