Yan G, Lan Y, Sun J, Xu T, Wei T, Qian PY. Comparative transcriptomic analysis of
in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences.
iScience 2022;
25:104092. [PMID:
35402864 PMCID:
PMC8983377 DOI:
10.1016/j.isci.2022.104092]
[Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/13/2022] [Accepted: 03/14/2022] [Indexed: 11/19/2022] Open
Abstract
Precise gene expression reflects the molecular response of deep-sea organisms to their harsh living environments. However, changes in environmental factors during lifting samples from the deep sea to a research vessel can also affect gene expression. By using the transcriptomic approach, we compared the gene expression profiles of the onboard fixed with the in situ fixed samples of the deep-sea limpet Bathyacmaea lactea. Our results revealed that the concomitant stress during conventional deep-sea sampling without RNA in situ fixation greatly influenced the gene expression. Various biological activities, such as cell and tissue structure, lysosomal activity, fluid balance, and unsaturated fatty acid metabolism, were perturbed, suggesting that the sampling stress has exerted systemic impacts on the life of the limpets. These findings clearly illustrate that deep-sea samples without RNA in situ fixation can easily lead to biased results in gene expression analysis, which requires to be appropriately addressed in future studies.
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