References
- Anders S, Paul Theodor P, Wolfgang H (2015) HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166–69.
- Andrews S (2010) FastQC: A quality control tool for high throughput sequence data. Bioinformatics.
http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ . - Auwera G, O’Connor BD (2020) Genomics in the Cloud, Sebastopol, CA: O’Reilly Media.
- Beheshti A, Cekanaviciute E, Smith DJ, Costes SV (2018) Global transcriptomic analysis suggests carbon dioxide as an environmental stressor in spaceflight: A systems biology GeneLab case study. Scientific Reports 8: 4191.
- Beisel NS, Noble J, Barbazuk WB, Anna-Lisa P, Ferl RJ (2019) Spaceflight-induced alternative splicing during seedling development in Arabidopsis Thaliana. NPJ Microgravity 5: 9.
- Benjamin D, Sato T, Cibulskis K, Getz G, Stewart C, Lichtenstein L (2019) Calling somatic SNVs and indels with Mutect2. bioRxiv.
https://doi.org/10.1101/861054 . - Besaratinia A, Synold TW, Xi B, Pfeifer GP (2004) G-to-T transversions and small tandem base deletions are the hallmark of mutations induced by ultraviolet a radiation in mammalian cells. Biochemistry 43: 8169–77.
- Bourdarie S, Xapsos M (2008) The near-Earth space radiation environment. IEEE Transactions on Nuclear Science 55: 1810–32.
- Broad Institute (2016) Picard, Broad Institute.
https://github.com/broadinstitute/picard . - Brojakowska A, Kour A, Thel MC, Park E, Bisserier M, Garikipati VNS, Hadri L, Mills PJ, Walsh K, Goukassian DA (2022) Retrospective analysis of somatic mutations and clonal hematopoiesis in astronauts. Communications Biology 5: 828.
- Califar B, Tucker R, Cromie J, Sng N, Schmitz RA, Callaham JA, Barbazuk B, Paul AL, Ferl RJ (2018) Approaches for surveying cosmic radiation damage in large populations of Arabidopsis Thaliana Seeds – antarctic balloons and particle beams. Gravitational and Space Research: Publication of the American Society for Gravitational and Space Research 6: 54–73.
- Chandler JO, Haas FB, Khan S, Bowden L, Ignatz M, Enfissi EMA, Gawthrop F, Griffiths A, Fraser PD, Rensing SA, Leubner-Metzger G (2020) Rocket science: The effect of spaceflight on germination physiology, ageing, and transcriptome of Eruca Sativa Seeds. Life (Basel, Switzerland) 10: 49.
- Cheng CY, Krishnakumar V, Chan AP, Thibaud-Nissen F, Schobel S, Town CD (2017) Araport11: A complete reannotation of the Arabidopsis Thaliana reference genome. The Plant Journal: For Cell and Molecular Biology 89: 789–804.
- Choi WG, Barker RJ, Kim SH, Swanson SJ, Gilroy S (2019) Variation in the transcriptome of different ecotypes of Arabidopsis Thaliana reveals signatures of oxidative stress in plant responses to spaceflight. American Journal of Botany 106: 123–36.
- Cucinotta FA, Schimmerling W, Wilson JW, Peterson LE, Badhwar GD, Saganti PB, Dicello JF (2001) Space radiation cancer risks and uncertainties for Mars missions. Radiation Research 156: 682–88.
- Cucinotta FA (2014) Space radiation risks for astronauts on multiple International Space Station missions. PloS One 9: e96099.
- Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: Ultrafast universal RNA-Seq aligner. Bioinformatics (Oxford, England) 29: 15–21.
- Dobin A, Gingeras TR (2016) Optimizing RNA-Seq mapping with STAR. Methods in Molecular Biology 1415: 245–62.
- Durante M (2014) Space radiation protection: Destination Mars. Life Sciences in Space Research 1: 2–9.
- Ebbert MTW, Wadsworth ME, Staley LA, Hoyt KL, Pickett B, Miller J, Duce J (2016) Alzheimer’s disease neuroimaging initiative. In Evaluating the Necessity of PCR Duplicate Removal from next-Generation Sequencing Data and a Comparison of Approaches, J.S.K. Kauwe, and P.G. Ridge (ed), p. 238. BMC Bioinformatics.
- Hannon GJ (2010) FASTX-Toolkit,
http://hannonlab.cshl.edu/fastx_toolkit . - Hellweg CE, Baumstark-Khan C (2007) Getting ready for the manned mission to Mars: The astronauts’ risk from space radiation. The Science of Nature 94: 517–26.
- Kennedy AR (2014) Biological effects of space radiation and development of effective countermeasures. Life Sciences in Space Research 1: 10–43.
- Kovalchuk O, Dubrova YE, Arkhipov A, Hohn B, Kovalchuk I (2000) Wheat mutation rate after Chernobyl. Nature 407: 583–84.
- Kunz BA, Armstrong JD (1998) Differences in the mutational specificities of sunlight and UVB radiation suggest a role for transversion-inducing DNA damage in solar photocarcinogenesis. Mutation Research 422: 77–83.
- Land ES, Sheppard J, Doherty CJ, Perera IY (2023) Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments. Frontiers in Plant Science 14: 1308713.
- La Tessa C, Sivertz M, Chiang IH, Lowenstein D, Rusek A (2016) Overview of the NASA space radiation laboratory. Life Sciences in Space Research 11: 18–23.
- Maruzani R, Brierley L, Jorgensen A, Fowler A (2024) Benchmarking UMI-aware and standard variant callers for low frequency ctDNA variant detection. BMC Genomics 25: 827.
- Møller AP, Mousseau TA (2013) The effects of natural variation in background radioactivity on humans, animals and other organisms: Evolution and natural variation in radioactivity. Biological Reviews of the Cambridge Philosophical Society 88: 226–54.
- Moreno-Villanueva M, Wong M, Lu T, Zhang Y, Wu H (2017) Interplay of space radiation and microgravity in DNA damage and DNA damage response. NPJ Microgravity 3: 14.
- Mousseau TA, Møller AP (2020) Plants in the light of ionizing radiation: What have we learned from Chernobyl, Fukushima, and other ‘hot’ places. Frontiers in Plant Science 11: 552.
- Ou X, Long L, Wu Y, Yu Y, Lin X, Qi X, Liu B (2010) Spaceflight-induced genetic and epigenetic changes in the rice (Oryza Sativa L.) genome are independent of each other. Genome 53: 524–32.
- Perera I, Sheppard JV, Land E (2019) The effect of spaceflight on transgenic Arabidopsis Plants with compromised signaling. NASA GeneLab.
https://doi.org/10.26030/WDTZ-V612 . - Perera IY, Hung CY, Brady S, Muday GK, Boss WF (2006) A universal role for inositol 1,4,5-trisphosphate-mediated signaling in plant gravitropism. Plant Physiology 140: 746–60.
- Poplin R, Ruano-Rubio V, DePristo MA, Fennell TJ, Carneiro MO, Van der Auwera GA, Kling DE, Gauthier LD, Levy-Moonshine A, Roazen D, Shakir K, Thiabault J, Chandran S, Whelan C, Lek M, Gabriel S, Daly MJ, Neale B, MacArthur DG, Banks E (2017) Scaling accurate genetic variant discovery to tens of thousands of samples. bioRxiv.
https://doi.org/10.1101/201178 . - Ray S, Gebre S, Fogle H, Berrios DC, Tran PB, Galazka JM, Costes SV (2019) GeneLab: Omics database for spaceflight experiments. Bioinformatics (Oxford, England) 35: 1753–59.
- R Core Team. n.d. R: A Language and Environment for Statistical Computing,
https://www.R-project.org/ . - Rinaldi A (2016) Research in space: In search of meaning: Life science research aboard the International Space Station has come under scrutiny for its costs and apparent lack of returns. EMBO Reports 17: 1098–1102.
- Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (Oxford, England) 26: 139–40.
- Sayols S, Scherzinger D, Klein H (2016) dupRadar: A bioconductor package for the assessment of PCR artifacts in RNA-Seq data. BMC Bioinformatics 17: 428.
- Sheppard J, Land ES, Toennisson TA, Doherty CJ, Perera IY (2021) Uncovering transcriptional responses to fractional gravity in Arabidopsis Roots. Life (Basel, Switzerland) 11: 1010.
- Thirsk R, Kuipers A, Mukai C, Williams D (2009) The space-flight environment: The International Space Station and beyond. Journal de l’Association Medicale Canadienne [Canadian Medical Association Journal] 180: 1216–20.
- Vandenbrink JP, Kiss JZ (2016) Space, the final frontier: A critical review of recent experiments performed in microgravity. Plant Science: An International Journal of Experimental Plant Biology 243: 115–19.
- Wuest SL, Richard S, Kopp S, Grimm D, Egli M (2015) Simulated microgravity: Critical review on the use of random positioning machines for mammalian cell culture. BioMed Research International 2015: 971474.
- Xu P, Chen H, Jin J, Cai W (2018) Single-base resolution methylome analysis shows epigenetic changes in Arabidopsis seedlings exposed to microgravity spaceflight conditions on board the SJ-10 recoverable satellite. NPJ Microgravity 4: 12.
- Yuge L, Kajiume T, Tahara H, Kawahara Y, Umeda C, Yoshimoto R, Wu SL, Yamaoka K, Asashima M, Kataoka K, Ide T (2006) Microgravity potentiates stem cell proliferation while sustaining the capability of differentiation. Stem Cells and Development 15: 921–29.
- Zhang LF (2001) Vascular adaptation to microgravity: What have we learned. Journal of Applied Physiology (Bethesda, Md.: 1985) 91: 2415–30.
- Zhang Y, Richards JT, Hellein JL, Johnson CM, Woodall J, Sorenson T, Neelam S, Ruby AMJ, Levine HG (2022) NASA’s ground-based microgravity simulation facility. Methods in Molecular Biology 2368: 281–99.