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NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data.
Overbey, Eliah G; Saravia-Butler, Amanda M; Zhang, Zhe; Rathi, Komal S; Fogle, Homer; da Silveira, Willian A; Barker, Richard J; Bass, Joseph J; Beheshti, Afshin; Berrios, Daniel C; Blaber, Elizabeth A; Cekanaviciute, Egle; Costa, Helio A; Davin, Laurence B; Fisch, Kathleen M; Gebre, Samrawit G; 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 S; Rosenthal, Sara Brin; Strong, Michael; Szewczyk, Nathaniel J; 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.
Afiliação
  • Overbey EG; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
  • Saravia-Butler AM; Logyx, LLC, Mountain View, CA 94043, USA.
  • Zhang Z; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Rathi KS; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA.
  • Fogle H; Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA 19104, USA.
  • da Silveira WA; The Bionetics Corporation, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Barker RJ; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Bass JJ; Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK.
  • Beheshti A; Department of Botany, University of Wisconsin, Madison, WI 53706, USA.
  • Berrios DC; 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.
  • Blaber EA; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Cekanaviciute E; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
  • Costa HA; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Davin LB; Center for Biotechnology and Interdisciplinary Studies, Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
  • Fisch KM; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Gebre SG; Departments of Pathology, and of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Geniza M; Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
  • Gilbert R; Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
  • Gilroy S; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Hardiman G; KBR, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Herranz R; Phylos Bioscience, Portland, OR 97214, USA.
  • Kidane YH; NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Kruse CPS; Department of Botany, University of Wisconsin, Madison, WI 53706, USA.
  • Lee MD; Institute for Global Food Security (IGFS) & School of Biological Sciences, Queen's University Belfast, Belfast, UK.
  • Liefeld T; Medical University of South Carolina, Charleston, SC, USA.
  • Lewis NG; Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
  • McDonald JT; Center for Pediatric Bone Biology and Translational Research, Texas Scottish Rite Hospital for Children, 2222 Welborn St., Dallas, TX 75219, USA.
  • Meller R; Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA.
  • Mishra T; Exobiology Branch, NASA Ames Research Center, Mountain View, CA 94035, USA.
  • Perera IY; Blue Marble Space Institute of Science, Seattle, WA 98154, USA.
  • Ray S; Department of Medicine, University of California San Diego, San Diego, CA 92093, USA.
  • Reinsch SS; Institute of Biological Chemistry, Washington State University, Pullman, WA 99164, USA.
  • Rosenthal SB; Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC 20007, USA.
  • Strong M; Department of Neurobiology and Pharmacology, Morehouse School of Medicine, Atlanta, GA 30310, USA.
  • Szewczyk NJ; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Tahimic CGT; Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA.
  • Taylor DM; NGM Biopharmaceuticals, South San Francisco, CA 94080, USA.
  • Vandenbrink JP; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA.
  • Villacampa A; Center for Computational Biology & Bioinformatics, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
  • Weging S; National Jewish Health, Center for Genes, Environment, and Health, 1400 Jackson Street, Denver, CO 80206, USA.
  • Wolverton C; Ohio Musculoskeletal and Neurological Institute and Department of Biomedical Sciences, Ohio University, Athens, OH 43147, USA.
  • Wyatt SE; Department of Biology, University of North Florida, Jacksonville, FL 32224, USA.
  • Zea L; 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.
  • Costes SV; Department of Biology, Louisiana Tech University, Ruston, LA 71272, USA.
  • Galazka JM; Centro de Investigaciones Biológicas Margarita Salas (CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain.
iScience ; 24(4): 102361, 2021 Apr 23.
Article em En | MEDLINE | ID: mdl-33870146
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.
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2021 Tipo de documento: Article
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Texto completo: 1 Base de dados: MEDLINE Idioma: En Ano de publicação: 2021 Tipo de documento: Article