On May 6, Dr. Sylvain Costes and Dr. Amanda Saravia-Butler presented, “GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization,” in a live webinar. Dr. Costes outlined the features of the GeneLab Data Systems and demonstrated how to search the repository, explore experimental metadata, download files, and use the visualization portal to identify differential expressed genes. In the second part of the webinar, Dr. Saravia-Butler demonstrated how to process RNA-seq data using the analysis platform. Due to technical issues, the speakers recorded their talks after the webinar. All questions asked during the session were collected and answered below.
View the webinar at: https://youtu.be/Kec5vXKRppw
Questions and Answers
1. Are there tutorials on the website?
Yes, there are several manuals and guides on how to use the system and analyze omics data, including step-by-step tutorials and videos. Check out the tutorials here: https://genelab.nasa.gov/help/tutorials
2. Is there a GeneLab data dictionary?
Yes, it will be publicly released in the near future. Controlled vocabulary and ontologies for fields throughout the metadata files were used. Contact us for a sneak preview: https://genelab.nasa.gov/help/contact
3. The research on genetical change in human body occurred while living in space center, how can I find articles about this research?
The publication, “The NASA Twins Study: A multidimensional analysis of a year-long human spaceflight,” is available here: https://science.sciencemag.org/content/364/6436/eaau8650
4. Is it possible to see the code that the visualization portals are using?
Genelab’s visualization code is not public yet. However, if interested contact GeneLab at: https://genelab.nasa.gov/help/contact
5. For the GeneLab for High School Summer Intern Program, will the focus be on spaceflight only or also on ground experiments etc.?
The GeneLab for High School Summer Intern Program will cover all types of experiments conducted by NASA including spaceflight and ground studies. For the full analysis and proposal, the focus will be primarily on spaceflight studies. For information on the intern program check out: https://www.nasa.gov/ames/genelab-for-high-schools
6. Are there any GeneLab resources on how best to perform comparative analysis between different model organisms?
The GeneLab team and the Analysis Working Groups are currently looking at various methods to perform such comparisons. Check out the GeneLab publications (listed below) to see the method used to compare datasets at the pathway level rather than the gene expression level. This alleviates the need of normalization across datasets. However, it is recognized that working at the gene level is also a critical aspect of such comparisons and GeneLab hopes to have some solutions in the near future. If interested in joining GeneLab’s Analysis Working Groups to look at this problem, contact us: https://genelab.nasa.gov/help/contact
GeneLab publications comparing multiple datasets:
- Multiomics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver
- NASA GeneLab Platform Utilized for Biological Response to Space Radiation in Animal Models
- GeneLab Database Analyses Suggest LongTerm Impact of Space Radiation on the Cardiovascular System by the Activation of FYN Through Reactive Oxygen Species
- Metaanalysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial “spaceflight response"
- Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study
- NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies
- A microRNA signature and TGFβ1 response were identified as the key master regulators for spaceflight awareness
- Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight
- Comparison of Bacillus subtilis transcriptome profiles from two separate missions to the International Space Station
A full list of publications is available here: https://genelab.nasa.gov/publications.
7. What is the best way to join a working group?
To join the Analysis Working Groups, please review this page https://genelab.nasa.gov/awg/join and send email to arc-dl-genelab-awg@mail.nasa.gov.
Other useful links
Webinar: https://youtu.be/Kec5vXKRppw
Contact speakers about webinar or GeneLab in general: https://genelab.nasa.gov/help/contact
Explore GeneLab spaceflight omics data: https://genelab.nasa.gov/
