Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences
Summary: 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...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2022-04-01
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| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004222003625 |
| _version_ | 1819026068219101184 |
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| author | Guoyong Yan Yi Lan Jin Sun Ting Xu Tong Wei Pei-Yuan Qian |
| author_facet | Guoyong Yan Yi Lan Jin Sun Ting Xu Tong Wei Pei-Yuan Qian |
| author_sort | Guoyong Yan |
| collection | DOAJ |
| description | Summary: 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. |
| first_indexed | 2024-12-21T05:20:42Z |
| format | Article |
| id | doaj.art-ce848178169f4dfab60be74c31897add |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-21T05:20:42Z |
| publishDate | 2022-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-ce848178169f4dfab60be74c31897add2022-12-21T19:14:49ZengElsevieriScience2589-00422022-04-01254104092Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differencesGuoyong Yan0Yi Lan1Jin Sun2Ting Xu3Tong Wei4Pei-Yuan Qian5Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, ChinaInstitute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao 266003, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, ChinaSouthern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China; Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China; Corresponding authorSummary: 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.http://www.sciencedirect.com/science/article/pii/S2589004222003625Biotehnologymarine biotechnologyomicsTranscriptomics |
| spellingShingle | Guoyong Yan Yi Lan Jin Sun Ting Xu Tong Wei Pei-Yuan Qian Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences iScience Biotehnology marine biotechnology omics Transcriptomics |
| title | Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences |
| title_full | Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences |
| title_fullStr | Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences |
| title_full_unstemmed | Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences |
| title_short | Comparative transcriptomic analysis of in situ and onboard fixed deep-sea limpets reveals sample preparation-related differences |
| title_sort | comparative transcriptomic analysis of in situ and onboard fixed deep sea limpets reveals sample preparation related differences |
| topic | Biotehnology marine biotechnology omics Transcriptomics |
| url | http://www.sciencedirect.com/science/article/pii/S2589004222003625 |
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