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Understanding Confounding Effects of Blood Handling Strategies on RNA Quality and Transcriptomic Alteration Using RNA Sequencing

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Abstract

Whole blood is one of the most widely utilized human samples in biological research and is useful for analyzing the mechanisms of diverse bio-molecular phenomena. However, owing to its fluidic properties, whole blood is relatively unstable in the frozen state compared to other samples. Because RNA is structurally unstable, sample damage can severely affect RNA quality, thereby reducing its usability. This study aimed to assess the quality of RNA which was prepared from blood stored at different temperatures and times prior to freezing, as well as the effect of long-term freezing. The quality of the RNA derived from different blood samples was assessed by measuring the RNA integrity number (RIN) and RNA sequencing to identify differentially expressed genes (DEGs, |fold-change (FC)|> 1.5, p < 0.05, false discovery rate (FDR) < 0.05) between the differently prepared RNA samples. We found that improper sample handling critically influenced both RNA quality and gene expression patterns. By suggesting the consequences, this study emphasizes the importance of sample management to obtain reliable downstream application outcomes.

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Acknowledgements

This study was supported by Korea Environmental Industry & Technology Institute (KEITI) through “the Environmental Health Action Program”, funded by Korea Ministry of Environment (MOE) (2017001360005)

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Authors and Affiliations

  1. Department of Bio-Nanotechnology, Hanyang University, 55, Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi, Republic of Korea

    Eun Jung Koh & Seung Hwan Kim

  2. Department of Molecular and Life Science, Hanyang University, 55, Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi, Republic of Korea

    So Yeon Yu & Seung Yong Hwang

  3. GeneTrigger, 20, Magokjungang 5-ro 1-gil, Gangseo-gu, Seoul, Republic of Korea

    Seung Jun Kim

  4. Department of Preventive Medicine, Korea University College of Medicine, 73, Goryeodae-ro, Seongbuk-gu, Seoul, Republic of Korea

    Eun-Il Lee

  5. Department of Applied Artificial Intelligence, Hanyang University, 55, Hanyangdaehak-ro, Sangnok-gu, Ansan, Gyeonggi, Republic of Korea

    Seung Yong Hwang

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  1. Eun Jung Koh
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Correspondence to Seung Yong Hwang.

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Koh, E.J., Yu, S.Y., Kim, S.H. et al. Understanding Confounding Effects of Blood Handling Strategies on RNA Quality and Transcriptomic Alteration Using RNA Sequencing. BioChip J 15, 187–194 (2021). https://doi.org/10.1007/s13206-021-00020-5

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  • DOI: https://doi.org/10.1007/s13206-021-00020-5

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