No. 23: New Data Submission Portal, Data Releases & COVID-19 Research

NASA GeneLab: Open Science for Life in Space


Newsletter No. 23: July 2020


Greetings from GeneLab!

In this issue:

New Software Release: GeneLab Environment for Online Data Entry

GeneLab’s latest software release includes new features and improvements to the study submission portal made available to the public on June 11, 2020. The GeneLab Environment for Online Data Entry (GEODE) is a web-based system that allows researchers to submit spaceflight and space-relevant omics data to be published in the Data Repository

GEODE provides GeneLab curators and users with a user-friendly platform to create, update, and submit a study for public release. New in this release are improved sample table controls, user profile management, and free text (custom) ontology. GeneLab curators are also now able to control the visibility of data files, link related studies, and configure a study to show visualization.


Powered by Metabolights, GeneLab has integrated and customized this tool for spaceflight omics data submission. This is the final major release of GEODE, with usability and improvement releases still to come.

New Workspace BETA

GeneLab’s latest software release also includes an all new redesign of the GeneLab Workspace. The new workspace is currently in BETA while the existing workspace is phased out. Come explore the new user interface at To access it, first login at



Rodent Research and GeneLab Investigate Effectiveness of New Rapid Freeze Hardware on Tissue Preservation

Results from transcriptomic analysis of liver tissues from the NASA Rodent Research-1 (RR-1) mission (GeneLab dataset GLDS-48) revealed that preservation method, not spaceflight, was the driving factor for gene expression changes among samples. Additionally, tissues processed from whole carcasses that were slow frozen at -80C had partially degraded transcripts, making it difficult to tease out which molecular pathways were altered by the space environment.

In response to these and other observations, the Rapid Freeze hardware, consisting of the Cryochiller and Glovebox freezer, was built by the University of Alabama at Birmingham for use on the International Space Station. The Rapid Freeze hardware reaches temperatures as low as -185°C, thereby freezing mouse tissues (Glovebox freezer) and whole carcasses (Cryochiller) at rates more closely mimicking those attained with immersion in liquid nitrogen.

To assess the ability of the Rapid Freeze system to preserve signals in gene expression data, the Rodent Research and GeneLab projects designed a ground study with three primary goals:
1) Evaluate the temperature profile of the Cryochiller and Glovebox freezer cartridges (Rapid Freeze hardware) over time during mock on-orbit procedures;
2) Determine the freezing profiles of tissues and carcasses using Rapid Freeze hardware at both optimal and sub-optimal temperatures (to mimic on-orbit operations), compared with those frozen in liquid nitrogen (the laboratory gold standard) or frozen at -80°C (the current standard method); and
3) Identify gene expression changes in a) tissues that were frozen via the Glovebox freezer and b) tissues dissected from whole or partial carcasses that were frozen via the Cryochiller versus tissues that were frozen via control methods (liquid nitrogen or -80°C slow freeze) to assess how the Rapid Freeze hardware compares with laboratory gold standard practices and our current standard methods. 

GeneLab’s Sample Processing Lab recently completed sequencing of the three rodent tissues evaluated using the Rapid Freeze hardware - spleen, liver, and soleus muscle. These raw RNA sequence data are now available in the GeneLab Data Repository. Check out and download the following data:

GLDS-272: Transcriptional analysis of spleens from mice preserved with the Rapid Freeze hardware

GLDS-273: Transcriptional analysis of livers from mice preserved with the Rapid Freeze hardware

GLDS-274: Transcriptional analysis of soleus from mice preserved with the Rapid Freeze hardware

Microbial Tracking-1 logo


Second COV-IRT Symposium Held

The second COV-IRT symposium on COVID-19 was held on July 17 and attended by more than 400 people, in addition to the almost 4000 views on Facebook Live. Co-led by GeneLab’s Afshin Beheshti from Ames Research Center and Todd Treangen from Rice University, this virtual Zoom symposium was hosted by Rice University. Among the attendees were officials from many government agencies including BARDA, DHS, CDC, DARPA, DoE, DoD, FDA, and NIH.

Read more…


GeneLab Scientist Interviewed by ABC News on COV-IRT

Afshin Beheshti


Afshin Beheshti was interviewed for a news story on his efforts with the NASA High Performance Computing (HPC) award to work on COVID-19 and his efforts with COVID-19 International Research Team COV-IRT. He discussed how the NASA HPC award given to him for this research can help improve our knowledge of COVID-19 and potentially lead to novel therapeutics against COVID-19. For the full interview click here.


GeneLab Webinar: New Discoveries Using GeneLab

Webinar - GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and VisualizationOn May 6, Sylvain Costes and Amanda Saravia-Butler gave a presentation entitled, “GeneLab: The NASA Systems Biology Platform for Space Omics Repository, Analysis and Visualization,” to over 80 participants in a live webinar. 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, Saravia-Butler demonstrated how to process RNA-seq data using the analysis platform. View the webinar here.  


Congratulations to the New HRP Grant Awardees

NASA selected 21 proposals to help answer questions about astronaut health and performance during future long-duration missions beyond low-Earth orbit. The proposals will investigate biological, physiological, and behavioral adaptations during spaceflight in support of NASA’s crewed Artemis missions to the Moon and future human exploration of Mars. Of the 21 proposals NASA selected, two research teams led by Sylvain Costes and Candice Tahimic were chosen in the Human Research Program’s recent selection. For more information click here.


Download 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 six such publications from late April – July 2020.

Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver – Nature

The influence of spaceflight on the astronaut salivary microbiome and the search for a microbiome biomarker for viral reactivation – Microbiome, Spring Nature

Microbiological and Nutritional Analysis of Lettuce Crops Grown on the International Space Station – Frontiers in Plant Science

Reproducible changes in the gut microbiome suggest a shift in microbial and host metabolism during spaceflight – Microbiome, Spring Nature

Spaceflight induces novel regulatory responses in Arabidopsis seedling as revealed by combined proteomic and transcriptomic analyses – BCM Plant Biology

Draft Genome Sequences of Tremellomycetes Strains Isolated from the International Space Station – ASM, Microbiology Resource Announcements


Spotlight on Newly Processed and Released GeneLab Data

Twenty-two new omics datasets have been added to GeneLab’s Data Repository for a total of 263 studies. Scroll through the list below for your favorite data type.
GeneLab model organisms


Upcoming Events

GeneLab will participate in two upcoming virtual conferences, ISSR&D and ASGSR. Join us!

ISSR&D – International Space Station Research & Development

From Vision to Discovery
Thursday, September 17, 2-3pm, PST

Maximizing Spaceflight Biological Data with Omics Analytics: The NASA GeneLab Database

Sylvain Costes, GeneLab Project Manager, NASA Ames Research Center
Samrawit Gebre, GeneLab Deputy Project Manager, NASA, NASA Ames Research Center


ASGSR – American Society for Gravitational and Space Research

The 2020 Virtual ASGSR Annual Meeting 
November 6, 1:30-2:45pm, PST
GeneLab and Physical Sciences Informatics Science (concurrent sessions)
GeneLab Team and AWG Members
Watch the GeneLab website for further information.


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Until the October Newsletter, stay healthy!

The GeneLab Team