No. 24: AWG Grant Awards, New Investigation with GeneLab Data, Standardizing Sample Processing and Sequencing

Newsletter No. 24: November 2020

Greetings from GeneLab!

New GeneLab Publications

Good science is never done alone. The primary goal of GeneLab is to bring together a community of scientists to utilize spaceflight and spaceflight-analog datasets hosted on GeneLab in order to generate novel discoveries and hypothesis-driven, collaborative, follow-on investigations, and data analysis that often lead to published manuscripts summarizing new discoveries. Below is a list of such publications from late August – October 2020:

NASA GeneLab: interfaces for the exploration of space omics data – Oxford Academic

Comparisons of Transcriptome Profiles from Bacillus subtilis Cells Grown in Space versus High Aspect Ratio Vessel (HARV) Clinostats Reveal a Low Degree of Concordance – Astrobiology

From target identification to drug development in space: Using the microgravity assist – Current Drug Discovery Technologies

Spotlight on Newly Processed and Released GeneLab Data

Twenty new omics datasets have been added to GeneLab’s Data Repository for a total of 283 studies. Click on this link for your favorite data type.

Sequencing for Spaceflight Samples

GeneLab’s Sample Processing Team utilizes Standard Operating Procedures (SOPs) for sample processing and sequencing of tissues and other biological samples into molecular analytes for molecular characterization. GeneLab’s sample processing procedures all have protocols that are organized into sections based on the order they occur overall creating a published workflow. Standardizing protocols allows for consistent results across multiple users while working with various tissue types. A new SOP collection is now publicly available on the GeneLab Sample Processing Github page. The project hopes that this collection of SOPs will act as a standard for all projects processing spaceflight samples. Increased communication and consistency between different laboratories in both industry and academia will allow for better availability of omics data from the limited and unique spaceflight experiments.

Multi-omics, Cross-species Analysis of GeneLab Data Leads to New NASA Investigation

A collaboration between NASA GeneLab and the Gilroy Lab has led to a multi-omics, cross-species analysis of GeneLab omics data, creating a new NASA Space Biology sponsored investigation into the effects of spaceflight and microgravity simulations on plant-microbe interactions.
A suite of visualization tools to explore relationships between studies within the GeneLab data repository has been created by Richard Barker, a member of the Gilroy Lab at the University of Wisconsin, Madison, and co-lead of the GeneLab Plant Analysis Working Group (AWG). These apps aggregate diverse data types and allow users to find associations between the distinct GeneLab accessions. This has allowed the identification of new correlations in the data leading to the generation of novel hypotheses and the creation of protocols for experimental validation. Read more.

Submission Portal

A new tutorial on how to submit omics data through the OSDR, has just been released. Follow the easy-to-use steps to create a user account and a data study. Check it out!

Plant Analysis Working Group Hosts International Virtual Hack-A-Thon

NASA’s GeneLab Plants Analysis Working Group (AWG) hosted its first international virtual hack-a-thon on August 5, 2020. Attended by 17 bioinformaticians from the US, UK, and Spain, hack-a-thon participants set out to use GeneLab’s database to dissect and quantify the specific gene expression responses of plants to spaceflight conditions. Thanks to the extensively curated data and metadata available in GeneLab’s repository, the spaceflight community now has an unprecedented capability to perform integrative analyses using the varied data produced by spaceflight experiments.  The Hack-a-thon was organized and hosted by Colin Kruse, along with co-hosts Richard Barker and Pankaj Jaiswal. Read more.

GeneLab at ISSR&D

On September 17, 2020, GeneLab participated in the ISSR&D Conference 2020 Online Series. GeneLab Project Manager Sylvain Costes presented, Maximizing Spaceflight Biological Data with Omics Analytics: The NASA GeneLab Database. Samrawit Gebre, GeneLab deputy project manager, demonstrated the use of the repository with smart search capability, an online controlled-access tool shed “Galaxy” to process user data with vetted standard workflows, a workspace for data sharing, and a data submission portal with ontology control for better metadata curation. The GeneLab visualization portal was also demonstrated, showing how anyone without formal training in bioinformatics can now browse the space biology omics data to discover new biology and potential solutions to improve life in space.

To listen to the talk go to: https://www.issconference.org/

Congratulations AWG Members for Space Biology Awards

Four GeneLab Analysis Working Group (AWG) members submitted Space Biology research proposals that were selected to “Advance Scientific Knowledge of Life in Space and Foster Human Space Exploration.”

Awards for Plant Biology Studies:
Chris Wolverton, Ph.D. Ohio Wesleyan University: RNA-Seq Guided Mutant Analysis to Discover New Components of Gravity Signaling in Plants
Simon Gilroy, Ph.D. University Of Wisconsin, Madison: Spaceflight Effects on Plant-Microbe Interactions

Award for Microbiology Studies:
Camilla Urbaniak, Ph.D. ZIN Technologies, Inc: Microgravity Analogs as Proxies for Spaceflight to Validate Biofilm Formation and the Exchange of Genes Between Organisms

Award for Postdoctoral Fellowship:
Eliah Overbey (PI: Christopher Mason, Ph.D.) Weill Medical College of Cornell University: High-resolution, murine spatial transcriptome mapping of the impact of spaceflight

Click here for additional information.

Upcoming Event

GeneLab will participate in the Australian Space Biology Symposium on November 18. Register to hear the talk.

Australian Space Biology Symposium
2^nd Australian Space Biology Symposium
November 18, 2020
Maximizing Spaceflight Biological Data with Omics Analytics: The NASA GeneLab Database
Sylvain Costes and Samrawit Gebre

Happy Holidays! Stay safe and healthy.

The GeneLab Team

	Stay connected with the NASA Open Science Data Repository: