GeneLab’s Sample Processing Lab Receives State-of-the-Art Nucleotide Sequencer
GeneLab receives new Illumina NovaSeq 6000 at NASA Ames.
GeneLab received an Illumina NovaSeq 6000 sequencing instrument. This state-of-the art sequencer can generate 3 trillion bases of sequencing data every two days (6 Tb of data), and will be used by GeneLab to maximize the data and knowledge generated from precious biological spaceflight experiments.
The project’s Sample Processing Lab successfully completed a RNAseq validation run on this machine, generating high-quality raw sequencing data. GeneLab will now focus on producing data from spaceflight and spaceflight-relevant samples. Data generated with this machine will begin appearing on GeneLab in the coming year.
GeneLab Collaboration Enables Generation of New Data
GeneLab is proud to announce the release of data from a collaboration with Dr. Xiao Mao of Loma Linda University. The collaboration provided supplemental funding for multi-omic analyses of multiple tissues from the ground study entitled, “Role of Oxidative Stress in Mediating the Effects of Combined Exposure to Simulated Microgravity and Radiation on Neurovascular Remodeling in Mouse (NNX13AL97G),” funded by NASA’s Space Biology program. The longitudinal study examined the independent and combined responses to low dose radiation and hind-limb unloading as a surrogate for spaceflight.
This GeneLab collaboration has enabled the generation of transcriptomic and epigenomic (Reduced Representation Bisulfite Sequencing) data from retina and brain samples published in GLDS-202 and GLDS-203, respectively, as well as transcriptomic data from skin and spleen that will be published at a later date. A full summary of the experiment is available in NASA’s Taskbook.
New Datasets Added to Data Repository
Check it out – 8 new datasets are available and ready for download from the GeneLab Data Repository:
GLDS-202: Low dose (0.4 Gy) irradiation (LDR) and hindlimb unloading (HLU) microgravity in mice (RNA-Seq)
GLDS-201: Impact of Antiorthostatic Suspension on Mouse response to Tetanus Toxoid and CpG
GLDS-183: Radiation-induced bystander effects and gene expression in cells deficient for RAD9
GLDS-182: Human skin fibroblast mitochondrial depletion, 0.5 Gy alpha-particle
GLDS-176: IMR90 bystander experiment 0.5 Gy alpha particle
GLDS-175: IMR90 4hr bystander experiment 0.5Gy alpha particle strip dish format
GLDS-170: NASA Aircraft Bioaerosol Collector (ABC)
NASA Produces New GeneLab Video
To educate the science community on the new space biology research capabilities and data available through GeneLab, NASA released a new video describing the GeneLab project. The NASA GeneLab video was created by Nicole Rose (ISS Research Video Producer, JSC), Rachel Barry (Communications Managing Editor, ISS Program Science Office, JSC), Amanda Saravia-Butler (Scientist, GeneLab Project, ARC) and Sandy Dueck (Science Communications Lead, GeneLab Project, ARC).
GeneLab Analysis Platform
GeneLab recently delivered a data analysis platform that allows anyone to analyze omics data from the GeneLab Data Repository or their own space-related experiments. This platform includes tools for processing sequence data, differential gene expression, and epigenetic analyses. Last month, at ASGSR, the GeneLab team held several training sessions to demonstrate how to perform RNA-Seq Analysis using this new platform. If you missed the training session, watch the video above to learn how to analyze RNA-Seq data.
GeneLab Publications 2018
The science community recently published 10 papers using omics data from the GeneLab Data Repository.
Singh NK, Bezdan D, Sielaff AC, Wheeler K, Mason CE, Venkateswaran K. Multi-drug resistant Enterobacter bugandensis species isolated from the International Space Station and comparative genomic analyses with human pathogenic strains. BMC Microbiol. 2018; 18(1):175.
Morrison MD and Nicholson WL. Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial ‘spaceflight response’. Sci Rep. 2018; 8(1):14403.
Ray S, Gebre S, Fogle H, Berrios D, Tran PB, Galazka JM,Costes SV. GeneLab: Omics database for spaceflight experiments. Bioinformatics. 2018; in press.
Beheshti A, Shirazi-Fard Y, Choi S, Berrios D, Gebre SG, Galazka JM, Costes SV. Exploring the Effects of Spaceflight on Mouse Physiology using the Open Access NASA GeneLab Platform. JoVE. 2018; in press.
Krishnamurthy A, Ferl RJ, Paul A-L. Comparing RNA-Seq and microarray gene expression data in two zones of the Arabidopsis root apex relevant to spaceflight. Appl Plant Sci. 2018; 6(11):e01197.
Singh NK, Wood JM, Karouia F, Venkateswara K. Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station Environmental Surfaces. Microbiome. 2018; 6(1):204.
Kamal KY, Herranz R, van Loon JJWA, Medina FJ. Cell cycle acceleration and changes in essential nuclear functions induced by simulated microgravity in a synchronized Arabidopsis cell culture. Plant Cell Environ. 2018; in press.
Beheshti A, Cekanaviciute E, Smith DJ, Costes SV. Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A GeneLab Case Study. Sci Rep. 2018; 8(1):4191.
Beheshti A, Miller J, Kidane Y, Berrios D, Gebre SG, Costes SV. NASA GeneLab Project: Bridging Space Radiation Omics with Ground Studies Project. Radiat Res. 2018; 189(6):553.
Beheshti A, Ray S, Fogle H, Berrios D, Costes SV. A microRNA signature and TGF-β1 response were identified as the key master regulators for spaceflight response. PLoS One. 2018; 13(7):e0199621.
Happy Holidays! You’ll hear from us again in early 2019!
The GeneLab Team