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Nouvel A, Laget J, Duranton F, Leroy J, Desmetz C, Servais MD, de Préville N, Galtier F, Nocca D, Builles N, Rebuffat S, Lajoix AD. Optimization of RNA extraction methods from human metabolic tissue samples of the COMET biobank. Sci Rep 2021; 11:20975. [PMID: 34697345 PMCID: PMC8545963 DOI: 10.1038/s41598-021-00355-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Constitution of biobank of human tissues requires careful handling and storage of biological material, to guarantee the quality of samples. Tissue preparation is also critical for further applications such as transcriptomic profiling. In this study, our aim was to evaluate the impact of different disruption techniques (FastPrep-24 instrument, GentleMACS dissociator, and syringe/needle) and homogenizing buffers (RLT versus QIAzol) on RNA purity and quality of metabolic tissues (adipose tissues, liver and skeletal muscle) present in the COMET Biobank. For all homogenization methods used and tissue types, the A260/280 ratios reached values ≥ 1.8, which are in the range of what is found in human tissues and cell lines, while the A260/230 ratios were however ≤ 1.8, with the lowest value obtained with GentleMACS Dissociator. In addition, GentleMACS Dissociator combined with QIAzol reagent gave the highest RIN value and 28S/18S ratio for all tissues tested, except for muscle. Performing RT-qPCR, Ct values for different housekeeping genes can be influenced by extraction methods and RNA quality of samples. In conclusion, we have demonstrated that different disruption techniques and homogenizing buffers impact the purity and some quality markers of RNA, and can also impact quantification of mRNAs by RT-qPCR in human metabolic tissues.
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Affiliation(s)
- Agathe Nouvel
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Jonas Laget
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Flore Duranton
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France.,RD Néphrologie, 2 rue des Muriers, 34090, Montpellier, France
| | - Jérémy Leroy
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Caroline Desmetz
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | | | | | - Florence Galtier
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France.,Clinical Investigation Center 1411, Hôpital St Eloi, INSERM, University Hospital of Montpellier, 80 Avenue Augustin Fliche, 34295, Montpellier Cedex 5, France.,Department of Endocrinology, Lapeyronie Hospital, University Hospital of Montpellier, 371 avenue du Doyen Gaston Giraud, 34295, Montpellier Cedex 5, France
| | - David Nocca
- Department of Digestive Surgery, University Hospital of Montpellier, 80 Avenue Augustin Fliche, 34295, Montpellier Cedex 5, France
| | - Nicolas Builles
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, 80 Avenue Augustin Fliche, 34295, Montpellier Cedex 5, France
| | - Sandra Rebuffat
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Anne-Dominique Lajoix
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, 15 avenue Charles Flahault, 34093, Montpellier Cedex 5, France.
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