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Overbey EG, Das S, Cope H, Madrigal P, Andrusivova Z, Frapard S, Klotz R, Bezdan D, Gupta A, Scott RT, Park J, Chirko D, Galazka JM, Costes SV, Mason CE, Herranz R, Szewczyk NJ, Borg J, Giacomello S. Challenges and considerations for single-cell and spatially resolved transcriptomics sample collection during spaceflight. CELL REPORTS METHODS 2022; 2:100325. [PMID: 36452864 PMCID: PMC9701605 DOI: 10.1016/j.crmeth.2022.100325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have experienced rapid development in recent years. The findings of spaceflight-based scRNA-seq and SRT investigations are likely to improve our understanding of life in space and our comprehension of gene expression in various cell systems and tissue dynamics. However, compared to their Earth-based counterparts, gene expression experiments conducted in spaceflight have not experienced the same pace of development. Out of the hundreds of spaceflight gene expression datasets available, only a few used scRNA-seq and SRT. In this perspective piece, we explore the growing importance of scRNA-seq and SRT in space biology and discuss the challenges and considerations relevant to robust experimental design to enable growth of these methods in the field.
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Affiliation(s)
- Eliah G. Overbey
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
| | - Saswati Das
- Department of Biochemistry, Atal Bihari Vajpayee Institute of Medical Sciences & Dr. Ram Manohar Lohia Hospital, New Delhi, India
| | - Henry Cope
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
| | - Pedro Madrigal
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
| | - Zaneta Andrusivova
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Solène Frapard
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rebecca Klotz
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Daniela Bezdan
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen 72076, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, German
- yuri GmbH, Meckenbeuren, Germany
| | | | - Ryan T. Scott
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | | | | | - Jonathan M. Galazka
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Sylvain V. Costes
- Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
| | - Christopher E. Mason
- Weill Cornell Medicine, New York, NY, USA
- Institute for Computational Biomedicine, New York, NY, USA
- The Feil Family Brain and Mind Research Institute, New York, NY, USA
- The WorldQuant Initiative for Quantitative Prediction, New York, NY, USA
| | - Raul Herranz
- Centro de Investigaciones Biológicas Margarita Salas (CSIC), Madrid 28040, Spain
| | - Nathaniel J. Szewczyk
- School of Medicine, University of Nottingham, Derby DE22 3DT, UK
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Joseph Borg
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
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