Temporal RNA Integrity Analysis of Archived Spaceflight Biological Samples

Elizabeth Delgadillo Talburt, Alison J French, Danielle K Lopez, San-Huei Lai Polo, Valery Boyko, Marie T Dinh, Jon C Rask, Kaushik Chakravarty, Helen J Stewart

Abstract


In spaceflight experiments, model organisms are used to assess the effects of microgravity on specific biological systems. In many cases, only one biological system is of interest to the Principal Investigator. To maximize the scientific return of experiments, the remaining spaceflight tissue is categorized, documented, and stored in the biobank at NASA Ames Research Center, which is maintained by the Ames Life Science Data Archive (ALSDA). The purpose of this study is to evaluate the state of a sample set of tissues from the ALSDA biobank. Garnering information – such as downstream functional analysis for the generation of omics datasets – from tissues is, in part, dependent on the state of sample preservation. RNA integrity number (RIN) values were calculated for rodent liver tissues that were part of scientific payloads returned from the International Space Station. Rat livers from Spacelab Life Sciences 1 (SLS-1) and mouse livers from Commercial Biomedical Test Module 3 (CBTM-3), Rodent Research 1 (RR1), and Rodent Research 3 (RR3) were tested. It was found that mean RIN values from CBTM-3, RR1, and RR3 were suitable for downstream functional analysis (RIN > 5) while the mean RIN value for SLS-1 was not (RIN = 2.5 ± 0.1). Information from this study lays the foundation for future efforts in determining the types of assays that are most appropriate for different tissues in the ALSDA biobank and similar preservation facilities, which would aid in shaping the design of experiments.

References


Auer H, Lyianarachchi S, Newsom D, Klisovic M, Marcucci u, Kornacker K (2003) Chipping away at the

chip bias: RNA degradation in microarray analysis. Nature Genetics 35: 292-293

Florell S, Coffin C, Holden J, Zimmermann J, Gerwels J, Summers B, Jones D, Leachman S (2001)

Preservation of RNA for Functional Genomic Studies: A Multidisciplinary Tumor Bank Protocol. Modern Pathology 14:116-128

Gallego Romero I, Pai A, Tung J, Gilad Y (2014) Impact of RNA degradation on measurements of gene

expression. Biomedical Central Biology 12: 42

Ibberson D, Benes V, Muckenthaler M, Castoldi M (2009) RNA degradation compromises the reliability

of microRNA expression profiling. Biomedical Central Biotechnology 9: 102

Imbeaud S. (2005) Towards standardization of RNA quality assessment using user-independent

classifiers of microcapillary electrophoresis traces. Nucleic Acids Research 33: e56

Salazar M, Fernando L, Baig F, Harcum S (2013) The effects of protein solubility on the RNA Integrity

Number (RIN) for recombinant Escherichia coli. Biochemical Engineering Journal 79: 129-135

Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W,

Granzow M, Ragg T (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. Biomedical Centerl Molecular Biology 7: 3

Schroeder A, Mueller O, Stocker S, Salowsky R, Leiber M, Gassmann M, Lightfoot S, Menzel W,

Granzow M, Ragg T (2006) The RIN: an RNA integrity number for assigning integrity values to RNA measurements. Biomedical Central Molecular Biology 7: 3

Sigurgeirsson B, Emanuelsson O, Lundeberg J (2014) Sequencing Degraded RNA Addressed by 3' Tag

Counting. PLoS ONE 9: e91851

Srinivasan M, Sedmak D, Jewell S (2002) Effect of Fixatives and Tissue Processing on the Content and

Integrity of Nucleic Acids. The American Journal of Pathology 161: 1961-1971

Valledor L, Escandón M, Meijón M, Nukarinen E, Cañal M, Weckwerth W (2014) A universal protocol

for the combined isolation of metabolites, DNA, long RNAs, small RNAs, and proteins from plants and microorganisms. The Plant Journal 79: 173-180

Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow J, Dasari S, Vedell P, Barman P, Wang L, Weinshiboum

R, Jen J, Huang H, Kohli M, Kocher J (2016) Measure transcript integrity using RNA-seq data. Biomedical Central Bioinformatics 17: 58

Zeng W, Mortazavi A (2012) Technical considerations for functional sequencing assays. Nature

Immunology 13: 802-807


Full Text: PG. 44-53 -- PDF