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Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue

Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from va...

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Autores principales: Pelisek, Jaroslav, Yundung, Yankey, Reutersberg, Benedikt, Meuli, Lorenz, Rössler, Fabian, Rabin, Laetitia, Kopp, Reinhard, Zimmermann, Alexander
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10420000/
https://www.ncbi.nlm.nih.gov/pubmed/37568514
http://dx.doi.org/10.3390/jcm12155109
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author Pelisek, Jaroslav
Yundung, Yankey
Reutersberg, Benedikt
Meuli, Lorenz
Rössler, Fabian
Rabin, Laetitia
Kopp, Reinhard
Zimmermann, Alexander
author_facet Pelisek, Jaroslav
Yundung, Yankey
Reutersberg, Benedikt
Meuli, Lorenz
Rössler, Fabian
Rabin, Laetitia
Kopp, Reinhard
Zimmermann, Alexander
author_sort Pelisek, Jaroslav
collection PubMed
description Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (ACTB, GAPDH), ribosomal genes (18S, 28S), and long non-coding RNAs (MALAT1, H19). Our results show that RINs from diseased vascular tissue are low (2–4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA’s disintegration state, is a better decision-making aid in choosing samples for omics analyses.
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spelling pubmed-104200002023-08-12 Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue Pelisek, Jaroslav Yundung, Yankey Reutersberg, Benedikt Meuli, Lorenz Rössler, Fabian Rabin, Laetitia Kopp, Reinhard Zimmermann, Alexander J Clin Med Article Proper biobanking is essential for obtaining reliable data, particularly for next-generation sequencing approaches. Diseased vascular tissues, having extended atherosclerotic pathologies, represent a particular challenge due to low RNA quality. In order to address this issue, we isolated RNA from vascular samples collected in our Swiss Vascular Biobank (SVB); these included abdominal aortic aneurysm (AAA), peripheral arterial disease (PAD), healthy aorta (HA), and muscle samples. We used different methods, investigated various admission solutions, determined RNA integrity numbers (RINs), and performed expression analyses of housekeeping genes (ACTB, GAPDH), ribosomal genes (18S, 28S), and long non-coding RNAs (MALAT1, H19). Our results show that RINs from diseased vascular tissue are low (2–4). If the isolation of primary cells is intended, as in our SVB, a cryoprotective solution is a better option for tissue preservation than RNAlater. Because RNA degradation proceeds randomly, controls with similar RINs are recommended. Otherwise, the data might convey differences in RNA degradation rather than the expressions of the corresponding genes. Moreover, since the 18S and 28S genes in the diseased vascular samples were degraded and corresponded with the low RINs, we believe that DV200, which represents the total RNA’s disintegration state, is a better decision-making aid in choosing samples for omics analyses. MDPI 2023-08-03 /pmc/articles/PMC10420000/ /pubmed/37568514 http://dx.doi.org/10.3390/jcm12155109 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Pelisek, Jaroslav
Yundung, Yankey
Reutersberg, Benedikt
Meuli, Lorenz
Rössler, Fabian
Rabin, Laetitia
Kopp, Reinhard
Zimmermann, Alexander
Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue
title Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue
title_full Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue
title_fullStr Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue
title_full_unstemmed Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue
title_short Swiss Vascular Biobank: Evaluation of Optimal Extraction Method and Admission Solution for Preserving RNA from  Human Vascular Tissue
title_sort swiss vascular biobank: evaluation of optimal extraction method and admission solution for preserving rna from  human vascular tissue
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10420000/
https://www.ncbi.nlm.nih.gov/pubmed/37568514
http://dx.doi.org/10.3390/jcm12155109
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