Space travel places the human body under unique stresses. Astronauts can experience changes in muscle mass, bone density, immune function, and metabolism during spaceflight. To better understand these effects, scientists increasingly rely on large biological datasets, often called omics data, to study how living systems respond to space environments.

One particularly important approach is transcriptomics, which examines changes in gene expression by measuring RNA molecules. RNA sequencing has become a valuable tool for identifying which genes are activated or suppressed during spaceflight and understanding how organisms adapt, or fail to adapt, to space conditions.

Researchers at Ohio University describe a practical workflow for analyzing bulk RNA sequencing data generated from spaceflight experiments.

The chapter focuses on a step-by-step analysis pipeline built in R, one of the most widely used programming environments for transcriptomics and bioinformatics.

Bulk RNA sequencing remains a popular approach because it provides a broad view of gene activity across tissues while remaining relatively straightforward and cost effective compared with some more complex methods.

The pipeline walks researchers through the major steps involved in RNA sequencing analysis, helping users move from raw sequencing data to biological interpretation.

The workflow includes:

• Importing RNA sequencing datasets into R
• Processing transcriptomic data
• Evaluating gene expression changes
• Identifying dysregulated pathways and molecular responses
• Interpreting biological changes linked to spaceflight

Importantly, the authors provide the entire workflow as a single downloadable script, available through GitHub. Researchers can use it directly or modify it to fit their own experiments.

The pipeline was demonstrated using data from a real spaceflight experiment, providing a practical example of how transcriptomics can help reveal molecular responses to life in space.

As space biology continues to expand, tools like this may become increasingly important. With future missions involving longer stays in orbit and possible travel to the Moon and Mars, understanding how gene expression changes in space could help protect astronaut health and improve mission success.

The open-source nature of the workflow may also help more researchers enter the growing field of space omics and RNA sequencing analysis.

Availability – The pipeline is available at: https://github.com/williscrg/MiMB-Space-RNAseq-Pipeline