iScience (Apr 2021)
NASA GeneLab RNA-seq consensus pipeline: Standardized processing of short-read RNA-seq data
- Eliah G. Overbey,
- Amanda M. Saravia-Butler,
- Zhe Zhang,
- Komal S. Rathi,
- Homer Fogle,
- Willian A. da Silveira,
- Richard J. Barker,
- Joseph J. Bass,
- Afshin Beheshti,
- Daniel C. Berrios,
- Elizabeth A. Blaber,
- Egle Cekanaviciute,
- Helio A. Costa,
- Laurence B. Davin,
- Kathleen M. Fisch,
- Samrawit G. Gebre,
- Matthew Geniza,
- Rachel Gilbert,
- Simon Gilroy,
- Gary Hardiman,
- Raúl Herranz,
- Yared H. Kidane,
- Colin P.S. Kruse,
- Michael D. Lee,
- Ted Liefeld,
- Norman G. Lewis,
- J. Tyson McDonald,
- Robert Meller,
- Tejaswini Mishra,
- Imara Y. Perera,
- Shayoni Ray,
- Sigrid S. Reinsch,
- Sara Brin Rosenthal,
- Michael Strong,
- Nathaniel J. Szewczyk,
- Candice G.T. Tahimic,
- Deanne M. Taylor,
- Joshua P. Vandenbrink,
- Alicia Villacampa,
- Silvio Weging,
- Chris Wolverton,
- Sarah E. Wyatt,
- Luis Zea,
- Sylvain V. Costes,
- Jonathan M. Galazka
Affiliations
- Eliah G. Overbey
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Amanda M. Saravia-Butler
- Logyx, LLC, Mountain View, CA 94043, USA; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Zhe Zhang
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
- Komal S. Rathi
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA
- Homer Fogle
- The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Willian A. da Silveira
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK
- Richard J. Barker
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
- Joseph J. Bass
- MRC Versus Arthritis Centre for Musculoskeletal Ageing Research, Royal Derby Hospital, University of Nottingham & National Institute for Health Research Nottingham Biomedical Research Centre, Derby DE22 3DT, UK
- Afshin Beheshti
- KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Daniel C. Berrios
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Elizabeth A. Blaber
- Center for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
- Egle Cekanaviciute
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Helio A. Costa
- Departments of Pathology, and of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA
- Laurence B. Davin
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
- Kathleen M. Fisch
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Samrawit G. Gebre
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Matthew Geniza
- Phylos Bioscience, Portland, OR 97214, USA
- Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Simon Gilroy
- Department of Botany, University of Wisconsin, Madison, WI 53706, USA
- Gary Hardiman
- Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK; Medical University of South Carolina, Charleston, SC, USA
- Raúl Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- Yared H. Kidane
- Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219, USA
- Colin P.S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA
- Michael D. Lee
- Exobiology Branch, NASA Ames Research Center, Mountain View, CA 94035, USA; Blue Marble Space Institute of Science, Seattle, WA 98154, USA
- Ted Liefeld
- Department of Medicine, University of California San Diego, San Diego, CA 92093, USA
- Norman G. Lewis
- Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA
- J. Tyson McDonald
- Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC 20007, USA
- Robert Meller
- Department of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Tejaswini Mishra
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
- Imara Y. Perera
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
- Shayoni Ray
- NGM Biopharmaceuticals, South San Francisco, CA 94080, USA
- Sigrid S. Reinsch
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Sara Brin Rosenthal
- Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
- Michael Strong
- National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson Street, Denver, CO 80206, USA
- Nathaniel J. Szewczyk
- Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USA
- Candice G.T. Tahimic
- Department of Biology, University of North Florida, Jacksonville, FL 32224, USA
- Deanne M. Taylor
- Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia and the Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Joshua P. Vandenbrink
- Department of Biology, Louisiana Tech University, Ruston, LA 71272, USA
- Alicia Villacampa
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- Silvio Weging
- Institute of Computer Science, Martin-Luther University Halle-Wittenberg, Von-Seckendorff-Platz 1, Halle 06120, Germany
- Chris Wolverton
- Department of Botany and Microbiology, Ohio Wesleyan University, Delaware, OH, USA
- Sarah E. Wyatt
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA; Interdisciplinary Program in Molecular and Cellular Biology, Ohio University, Athens, OH 45701, USA
- Luis Zea
- BioServe Space Technologies, Aerospace Engineering Sciences Department, University of Colorado Boulder, Boulder 80303 USA
- Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Corresponding author
- Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA; Corresponding author
- Journal volume & issue
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Vol. 24,
no. 4
p. 102361
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.
