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1. Meta-analysis of the space flight and microgravity response of the Arabidopsis plant transcriptome

Author

NASA Astrobiology Institute (US), Agencia Estatal de Investigación (España), Oregon State University, Barker, Richard [0000-0001-5681-9857], Kruse, Colin P. S. [0000-0001-7070-8889], Saravia-Butler, Amanda M. [0000-0001-7505-2743], Fogle, Homer [0000-0002-5579-5432], Chang, Hyun-Seok [0000-0003-1151-5969], Kinscherf, Noah [0000-0001-8807-1089], Villacampa, Alicia [0000-0002-7398-8545], Manzano, Aranzazu [0000-0002-0150-0803], Herranz, Raúl [0000-0002-0246-9449], Davin, Laurence B. [0000-0002-3248-6485], Lewis, Norman G. [0000-0001-5742-032X], Perera, Imara Y. [0000-0001-9421-1420], Wolverton, Chris [0000-0003-2248-474X], Jaiswal, Pankaj [0000-0002-1005-8383], Reinsch, Sigrid, Wyatt, Sarah E. [0000-0001-7874-0509], Gilroy, Simon [0000-0001-9597-6839], Barker, Richard, Kruse, Colin P. S., Johnson, Christina, Saravia-Butler, Amanda M., Fogle, Homer, Chang, Hyun-Seok, Trane, Ralph Møller, Kinscherf, Noah, Villacampa, Alicia, Manzano, Aranzazu, Herranz, Raúl, Davin, Laurence B., Lewis, Norman G., Perera, Imara Y., Wolverton, Chris, Gupta, Parul, Jaiswal, Pankaj, Wyatt, Sarah E., Gilroy, Simon, NASA Astrobiology Institute (US), Agencia Estatal de Investigación (España), Oregon State University, Barker, Richard [0000-0001-5681-9857], Kruse, Colin P. S. [0000-0001-7070-8889], Saravia-Butler, Amanda M. [0000-0001-7505-2743], Fogle, Homer [0000-0002-5579-5432], Chang, Hyun-Seok [0000-0003-1151-5969], Kinscherf, Noah [0000-0001-8807-1089], Villacampa, Alicia [0000-0002-7398-8545], Manzano, Aranzazu [0000-0002-0150-0803], Herranz, Raúl [0000-0002-0246-9449], Davin, Laurence B. [0000-0002-3248-6485], Lewis, Norman G. [0000-0001-5742-032X], Perera, Imara Y. [0000-0001-9421-1420], Wolverton, Chris [0000-0003-2248-474X], Jaiswal, Pankaj [0000-0002-1005-8383], Reinsch, Sigrid, Wyatt, Sarah E. [0000-0001-7874-0509], Gilroy, Simon [0000-0001-9597-6839], Barker, Richard, Kruse, Colin P. S., Johnson, Christina, Saravia-Butler, Amanda M., Fogle, Homer, Chang, Hyun-Seok, Trane, Ralph Møller, Kinscherf, Noah, Villacampa, Alicia, Manzano, Aranzazu, Herranz, Raúl, Davin, Laurence B., Lewis, Norman G., Perera, Imara Y., Wolverton, Chris, Gupta, Parul, Jaiswal, Pankaj, Wyatt, Sarah E., and Gilroy, Simon

Abstract

Spaceflight presents a multifaceted environment for plants, combining the effects on growth of many stressors and factors including altered gravity, the influence of experiment hardware, and increased radiation exposure. To help understand the plant response to this complex suite of factors this study compared transcriptomic analysis of 15 Arabidopsis thaliana spaceflight experiments deposited in the National Aeronautics and Space Administration’s GeneLab data repository. These data were reanalyzed for genes showing significant differential expression in spaceflight versus ground controls using a single common computational pipeline for either the microarray or the RNA-seq datasets. Such a standardized approach to analysis should greatly increase the robustness of comparisons made between datasets. This analysis was coupled with extensive cross-referencing to a curated matrix of metadata associated with these experiments. Our study reveals that factors such as analysis type (i.e., microarray versus RNA-seq) or environmental and hardware conditions have important confounding effects on comparisons seeking to define plant reactions to spaceflight. The metadata matrix allows selection of studies with high similarity scores, i.e., that share multiple elements of experimental design, such as plant age or flight hardware. Comparisons between these studies then helps reduce the complexity in drawing conclusions arising from comparisons made between experiments with very different designs.

Published
2023

2. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

Author

National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, William A., Barker, Richard, Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit, Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P. S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, MichaelSzewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., Galazka, Jonathan M., National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Saravia-Butler, Amanda M., Zhang, Zhe, Rathi, Komal S., Fogle, Homer, da Silveira, William A., Barker, Richard, Bass, Joseph J., Beheshti, Afshin, Berrios, Daniel C., Blaber, Elizabeth A., Cekanaviciute, Egle, Costa, Helio A., Davin, Laurence B., Fisch, Kathleen M., Gebre, Samrawit, Geniza, Matthew, Gilbert, Rachel, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kidane, Yared H., Kruse, Colin P. S., Lee, Michael D., Liefeld, Ted, Lewis, Norman G., McDonald, J. Tyson, Meller, Robert, Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, MichaelSzewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Vandenbrink, Joshua P., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Zea, Luis, Costes, Sylvain V., and Galazka, Jonathan M.

Abstract

With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab.

Published
2021

3. A new era for space life science: international standards for space omics processing

Author

National Aeronautics and Space Administration (US), University of Nottingham, Japan Society for the Promotion of Science, Department of Biomedical and Health Informatics, Philadelphia, Children's Hospital of Philadelphia Research Institute, National Institutes of Health (US), Rutter, Lindsay [0000-0003-2123-3949], Bezdan, Daniela [0000-0002-1203-8239], Cope, Henry [0000-0002-4984-0567], Gabitto, Mariano [0000-0001-6911-344X], Gebre, Samrawit [0000-0002-8963-4856], Giacomello, Stefania [0000-0003-0738-1574], Gilroy, Simon [0000-0001-9597-6839], Green, Stefan J. [0000-0003-2781-359X], Mason, Christopher E. [0000-0002-1850-1642], Reinsch, Sigrid [0000-0002-6484-7521], Szewczyk, Nathaniel [0000-0003-4425-9746], Galazka, Jonathan M. [0000-0002-4153-0249], Herranz, Raúl [0000-0002-0246-9449], Muratani, Masafumi [0000-0002-0276-8000], Rutter, Lindsay, Barker, Richard, Bezdan, Daniela, Cope, Henry, Costes, Sylvain V., Degoricija, Lovorka, Fisch, Kathleen M., Gabitto, Mariano, Gebre, Samrawit, Giacomello, Stefania, Gilroy, Simon, Green, Stefan J., Mason, Christopher E., Reinsch, Sigrid, Szewczyk, Nathaniel, Taylor, Deanne M., Galazka, Jonathan M., Herranz, Raúl, Muratani, Masafumi, National Aeronautics and Space Administration (US), University of Nottingham, Japan Society for the Promotion of Science, Department of Biomedical and Health Informatics, Philadelphia, Children's Hospital of Philadelphia Research Institute, National Institutes of Health (US), Rutter, Lindsay [0000-0003-2123-3949], Bezdan, Daniela [0000-0002-1203-8239], Cope, Henry [0000-0002-4984-0567], Gabitto, Mariano [0000-0001-6911-344X], Gebre, Samrawit [0000-0002-8963-4856], Giacomello, Stefania [0000-0003-0738-1574], Gilroy, Simon [0000-0001-9597-6839], Green, Stefan J. [0000-0003-2781-359X], Mason, Christopher E. [0000-0002-1850-1642], Reinsch, Sigrid [0000-0002-6484-7521], Szewczyk, Nathaniel [0000-0003-4425-9746], Galazka, Jonathan M. [0000-0002-4153-0249], Herranz, Raúl [0000-0002-0246-9449], Muratani, Masafumi [0000-0002-0276-8000], Rutter, Lindsay, Barker, Richard, Bezdan, Daniela, Cope, Henry, Costes, Sylvain V., Degoricija, Lovorka, Fisch, Kathleen M., Gabitto, Mariano, Gebre, Samrawit, Giacomello, Stefania, Gilroy, Simon, Green, Stefan J., Mason, Christopher E., Reinsch, Sigrid, Szewczyk, Nathaniel, Taylor, Deanne M., Galazka, Jonathan M., Herranz, Raúl, and Muratani, Masafumi

Abstract

Space agencies have announced plans for human missions to the Moon to prepare for Mars. However, the space environment presents stressors that include radiation, microgravity, and isolation. Understanding how these factors affect biology is crucial for safe and effective crewed space exploration. There is a need to develop countermeasures, to adapt plants and microbes for nutrient sources and bioregenerative life support, and to limit pathogen infection. Scientists across the world are conducting space omics experiments on model organisms and, more recently, on humans. Optimal extraction of actionable scientific discoveries from these precious datasets will only occur at the collective level with improved standardization. To address this shortcoming, we established ISSOP (International Standards for Space Omics Processing), an international consortium of scientists who aim to enhance standard guidelines between space biologists at a global level. Here we introduce our consortium and share past lessons learned and future challenges related to spaceflight omics.

Published
2020

4. NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data

Author

Komal S. Rathi, Egle Cekanaviciute, Colin P.S. Kruse, Sara Brin Rosenthal, Eliah G. Overbey, Shayoni Ray, Robert Meller, Daniel C. Berrios, Ted Liefeld, Raúl Herranz, Gary Hardiman, Sarah E. Wyatt, Richard Barker, Kathleen M. Fisch, Norman G. Lewis, Matthew Geniza, Sylvain V. Costes, Amanda M. Saravia-Butler, Michael J. Strong, Laurence B. Davin, Simon Gilroy, Tejaswini Mishra, Chris Wolverton, Joshua P. Vandenbrink, Zhe Zhang, Michael D. Lee, Silvio Weging, Alicia Villacampa, Joseph J. Bass, Homer Fogle, Sigrid Reinsch, Elizabeth A. Blaber, Luis Zea, Rachel Gilbert, Jonathan M. Galazka, Willian A. da Silveira, J. Tyson McDonald, Samrawit G. Gebre, Yared H. Kidane, Nathaniel J. Szewczyk, Imara Y. Perera, Deanne Taylor, Helio A. Costa, Afshin Beheshti, Candice Tahimic, National Aeronautics and Space Administration (US), Biotechnology and Biological Sciences Research Council (UK), Centre for Musculoskeletal Ageing Research (UK), Agencia Estatal de Investigación (España), Nottingham Biomedical Research Centre (UK), Overbey, Eliah G. [0000-0002-2866-8294], Fogle, Homer [0000-0002-5579-5432], Beheshti, Afshin [0000-0003-4643-531X], Berrios, Daniel C. [0000-0003-4312-9552], Cekanaviciute, Egle [0000-0003-3306-1806], Davin, Laurence B. [0000-0002-3248-6485], Gebre, Samrawit [0000-0002-8963-4856], Geniza, Matthew [0000-0003-4828-7891], Gilroy, Simon [0000-0001-9597-6839], Hardiman, Gary [0000-0003-4558-0400], Herranz, Raúl [0000-0002-0246-9449], Kruse, Colin P. S. [0000-0001-7070-8889], Mishra, Tejaswini [0000-0001-9931-1260], Perera, Imara Y. [0000-0001-9421-1420], Ray, Shayoni [0000-0003-1911-7738], Reinsch, Sigrid [0000-0002-6484-7521], Rosenthal, Sara Brin [0000-0002-6548-9658], Strong, Michael [0000-0002-3247-6260], Szewczyk, Nathaniel [0000-0003-4425-9746], Tahimic, Candice G. T. [0000-0001-5862-2652], Taylor, Deanne M. [0000-0002-3302-4610], Villacampa, Alicia [0000-0002-7398-8545], Weging, Silvio [0000-0002-8484-4352], Wolverton, Chris [0000-0003-2248-474X], Wyatt, Sarah E. [0000-0001-7874-0509], Costes, Sylvain V. [0000-0002-8542-2389], Galazka, Jonathan M. [0000-0002-4153-0249], Overbey, Eliah G., Fogle, Homer, Beheshti, Afshin, Berrios, Daniel C., Cekanaviciute, Egle, Davin, Laurence B., Gebre, Samrawit, Geniza, Matthew, Gilroy, Simon, Hardiman, Gary, Herranz, Raúl, Kruse, Colin P. S., Mishra, Tejaswini, Perera, Imara Y., Ray, Shayoni, Reinsch, Sigrid, Rosenthal, Sara Brin, Strong, Michael, Szewczyk, Nathaniel, Tahimic, Candice G. T., Taylor, Deanne M., Villacampa, Alicia, Weging, Silvio, Wolverton, Chris, Wyatt, Sarah E., Costes, Sylvain V., and Galazka, Jonathan M.

Subjects
0301 basic medicine, Data processing, Multidisciplinary, Computer science, Science, Pipeline (computing), Analysis working, Omics, RNA-Seq, 02 engineering and technology, 021001 nanoscience & nanotechnology, Short read, computer.software_genre, Article, Transcriptome, 03 medical and health sciences, 030104 developmental biology, Differentially expressed genes, Gene expression, Data mining, 0210 nano-technology, Space Sciences, Gene, computer
Abstract

Summary With the development of transcriptomic technologies, we are able to quantify precise changes in gene expression profiles from astronauts and other organisms exposed to spaceflight. Members of NASA GeneLab and GeneLab-associated analysis working groups (AWGs) have developed a consensus pipeline for analyzing short-read RNA-sequencing data from spaceflight-associated experiments. The pipeline includes quality control, read trimming, mapping, and gene quantification steps, culminating in the detection of differentially expressed genes. This data analysis pipeline and the results of its execution using data submitted to GeneLab are now all publicly available through the GeneLab database. We present here the full details and rationale for the construction of this pipeline in order to promote transparency, reproducibility, and reusability of pipeline data; to provide a template for data processing of future spaceflight-relevant datasets; and to encourage cross-analysis of data from other databases with the data available in GeneLab., Graphical abstract, Highlights • Analysis of omics data from different spaceflight studies presents unique challenges • A standardized pipeline for RNA-seq analysis eliminates data processing variation • The GeneLab RNA-seq pipeline includes QC, trimming, mapping, quantification, and DGE • Space-relevant data processed with this pipeline are available at genelab.nasa.gov, Omics; Space Sciences

Published
2021
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5. A New Era for Space Life Science: International Standards for Space Omics Processing

Author

Jonathan M. Galazka, Sylvain V. Costes, Stefan J. Green, Richard Barker, Lindsay Rutter, Henry Cope, Deanne Taylor, Kathleen M. Fisch, Raúl Herranz, Stefania Giacomello, Daniela Bezdan, Samrawit G. Gebre, Christopher E. Mason, Mariano I. Gabitto, Lovorka Degoricija, Masafumi Muratani, Sigrid Reinsch, Simon Gilroy, Nathaniel J. Szewczyk, National Aeronautics and Space Administration (US), University of Nottingham, Japan Society for the Promotion of Science, Department of Biomedical and Health Informatics, Philadelphia, Children's Hospital of Philadelphia Research Institute, National Institutes of Health (US), Rutter, Lindsay, Bezdan, Daniela, Cope, Henry, Gabitto, Mariano, Gebre, Samrawit, Giacomello, Stefania, Gilroy, Simon, Green, Stefan J., Mason, Christopher E., Reinsch, Sigrid, Szewczyk, Nathaniel, Galazka, Jonathan M., Herranz, Raúl, Muratani, Masafumi, Rutter, Lindsay [0000-0003-2123-3949], Bezdan, Daniela [0000-0002-1203-8239], Cope, Henry [0000-0002-4984-0567], Gabitto, Mariano [0000-0001-6911-344X], Gebre, Samrawit [0000-0002-8963-4856], Giacomello, Stefania [0000-0003-0738-1574], Gilroy, Simon [0000-0001-9597-6839], Green, Stefan J. [0000-0003-2781-359X], Mason, Christopher E. [0000-0002-1850-1642], Reinsch, Sigrid [0000-0002-6484-7521], Szewczyk, Nathaniel [0000-0003-4425-9746], Galazka, Jonathan M. [0000-0002-4153-0249], Herranz, Raúl [0000-0002-0246-9449], and Muratani, Masafumi [0000-0002-0276-8000]

Subjects
Metadata, Twins study, Standardization, Omics, General Decision Sciences, Space (commercial competition), GeneLab, Data science, ESA, Space exploration, Perspective, ISSOP, NASA, JAXA, Space biology, Space environment
Abstract

10 p.-2 fig., Space agencies have announced plans for human missions to the Moon to prepare for Mars. However, the space environment presents stressors that include radiation, microgravity, and isolation. Understanding how these factors affect biology is crucial for safe and effective crewed space exploration. There is a need to develop countermeasures, to adapt plants and microbes for nutrient sources and bioregenerative life support, and to limit pathogen infection. Scientists across the world are conducting space omics experiments on model organisms and, more recently, on humans. Optimal extraction of actionable scientific discoveries from these precious datasets will only occur at the collective level with improved standardization. To address this shortcoming, we established ISSOP (International Standards for Space Omics Processing), an international consortium of scientists who aim to enhance standard guidelines between space biologists at a global level. Here we introduce our consortium and share past lessons learned and future challenges related to spaceflight omics., European (D.B., H.C., N.J.S., R.H., and S. Giacomello) contribution is supported by ESA Topical Team “Space Omics: Towards an integrated ESA/NASA –omics database for spaceflight and ground facilities experiments” grant 4000131202/20/NL/PG/pt to R.H. S. Giacomello is supported by Formas grant 2017-01066_3. H.C. is supported by the Horizon Centre for Doctoral Training at the University of Nottingham (UKRI grant no. EP/S023305/1) and by the NASA GeneLab Animal Analysis Working Group. N.J.S. is supported by the National Aeronautics and Space Administration (NNX15AL16G). NASA GeneLab members (J.M.G., S.V.C., S.S.R., L.D., S. Gebre) are supported by the NASA Space Biology program within the NASA Science Mission Directorate's (SMD) Biological and Physical Sciences (BPS) Division. R.B. and S. Gilroy are supported by NASA (80NSSC19K0132). L.R. and M.M. represent the Omics Subgroup of Japan Society for the Promotion of Science (JSPS) KAKENHI funding group Living in Space and are supported by JP15K21745, JP15H05940, and JP20H03234. L.R. is supported by JSPS postdoctoral fellowship P20382. D.T. is supported by the Department of Biomedical and Health Informatics and The Children’s Hospital of Philadelphia Research Institute. K.F. is supported by the UC San Diego Department of Medicine and National Institutes of Health, grant UL1TR001442 of CTSA (Clinical and Translational Science Awards). C.E.M. is funded from the WorldQuant Foundation, The Pershing Square Sohn Cancer Research Alliance, and the National Institutes of Health (R01MH117406).

Published
2020

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