MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits
Abstract Background Describing and evaluating miRNA inventories with Next Generation Sequencing is a goal of scientists from a wide range of fields. It requires high purity, high quality, and high yield RNA extractions that do not only contain abundant ribosomal RNAs but are also enriched in miRNAs....
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ftdoajarticles:oai:doaj.org/article:606311e758174aafa2d5fbb4c1b40497 2023-05-15T15:32:03+02:00 MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits Harris Philip Fromm Bastian Bachmann Lutz 2011-06-01T00:00:00Z https://doi.org/10.1186/1756-0500-4-217 https://doaj.org/article/606311e758174aafa2d5fbb4c1b40497 EN eng BMC http://www.biomedcentral.com/1756-0500/4/217 https://doaj.org/toc/1756-0500 doi:10.1186/1756-0500-4-217 1756-0500 https://doaj.org/article/606311e758174aafa2d5fbb4c1b40497 BMC Research Notes, Vol 4, Iss 1, p 217 (2011) Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 article 2011 ftdoajarticles https://doi.org/10.1186/1756-0500-4-217 2022-12-31T08:51:24Z Abstract Background Describing and evaluating miRNA inventories with Next Generation Sequencing is a goal of scientists from a wide range of fields. It requires high purity, high quality, and high yield RNA extractions that do not only contain abundant ribosomal RNAs but are also enriched in miRNAs. Here we compare 6 disparate and commercially available totalRNA extraction kits for their suitability for miRNA-preparations from Gyrodactylus salaris , an important but small (500 μm in length) monogenean pathogen of Norwegian Atlantic salmon ( Salmo salar ). Findings We evaluated 1 salt precipitation method (MasterPure™ Complete RNA Purification Kit, Epicentre), 2 Phenol based extraction methods (mirVana Kit, Ambion, and Trizol Plus Kit, Invitrogen), 1 paramagnetic bead extraction method (RNA Tissue kit, GeneMole) and 2 purification methods based on spin column chromatography using a proprietary resin as separation matrix (Phenol-free Total RNA Purification Kit, Amresco, and ZR MicroPrep Kit, Zymo Research). The quality of the extractions from 1, 10 and 100 individuals, respectively, was assessed in terms of totalRNA yield, RNA integrity, and smallRNA and miRNA yield. The 6 RNA extraction methods yielded considerably different total RNA extracts, with striking differences in low molecular weight RNA yield. The Phenol-free Total RNA Purification Kit (Amresco) showed the highest totalRNA yield, but the best miRNA/totalRNA ratio was obtained with the ZR MicroPrep Kit (Zymo Research). It was not possible to extract electrophoretically detectable miRNAs from Gyrodactylus salaris with the RNA Tissue Kit (GeneMole) or the Trizol Plus Kit (Invitrogen). Conclusions We present an optimized extraction protocol for single and small numbers of Gyrodactylus salaris from infected Atlantic salmon that delivers a totalRNA yield suitable for downstream next generation sequencing analyses of miRNA. Two of the six tested totalRNA kits/methods were not suitable for the extraction of miRNAs from Gyrodactylus salaris . Article in Journal/Newspaper Atlantic salmon Salmo salar Directory of Open Access Journals: DOAJ Articles BMC Research Notes 4 1 |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
language |
English |
topic |
Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 |
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Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 Harris Philip Fromm Bastian Bachmann Lutz MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits |
topic_facet |
Medicine R Biology (General) QH301-705.5 Science (General) Q1-390 |
description |
Abstract Background Describing and evaluating miRNA inventories with Next Generation Sequencing is a goal of scientists from a wide range of fields. It requires high purity, high quality, and high yield RNA extractions that do not only contain abundant ribosomal RNAs but are also enriched in miRNAs. Here we compare 6 disparate and commercially available totalRNA extraction kits for their suitability for miRNA-preparations from Gyrodactylus salaris , an important but small (500 μm in length) monogenean pathogen of Norwegian Atlantic salmon ( Salmo salar ). Findings We evaluated 1 salt precipitation method (MasterPure™ Complete RNA Purification Kit, Epicentre), 2 Phenol based extraction methods (mirVana Kit, Ambion, and Trizol Plus Kit, Invitrogen), 1 paramagnetic bead extraction method (RNA Tissue kit, GeneMole) and 2 purification methods based on spin column chromatography using a proprietary resin as separation matrix (Phenol-free Total RNA Purification Kit, Amresco, and ZR MicroPrep Kit, Zymo Research). The quality of the extractions from 1, 10 and 100 individuals, respectively, was assessed in terms of totalRNA yield, RNA integrity, and smallRNA and miRNA yield. The 6 RNA extraction methods yielded considerably different total RNA extracts, with striking differences in low molecular weight RNA yield. The Phenol-free Total RNA Purification Kit (Amresco) showed the highest totalRNA yield, but the best miRNA/totalRNA ratio was obtained with the ZR MicroPrep Kit (Zymo Research). It was not possible to extract electrophoretically detectable miRNAs from Gyrodactylus salaris with the RNA Tissue Kit (GeneMole) or the Trizol Plus Kit (Invitrogen). Conclusions We present an optimized extraction protocol for single and small numbers of Gyrodactylus salaris from infected Atlantic salmon that delivers a totalRNA yield suitable for downstream next generation sequencing analyses of miRNA. Two of the six tested totalRNA kits/methods were not suitable for the extraction of miRNAs from Gyrodactylus salaris . |
format |
Article in Journal/Newspaper |
author |
Harris Philip Fromm Bastian Bachmann Lutz |
author_facet |
Harris Philip Fromm Bastian Bachmann Lutz |
author_sort |
Harris Philip |
title |
MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits |
title_short |
MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits |
title_full |
MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits |
title_fullStr |
MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits |
title_full_unstemmed |
MicroRNA preparations from individual monogenean Gyrodactylus salaris -a comparison of six commercially available totalRNA extraction kits |
title_sort |
microrna preparations from individual monogenean gyrodactylus salaris -a comparison of six commercially available totalrna extraction kits |
publisher |
BMC |
publishDate |
2011 |
url |
https://doi.org/10.1186/1756-0500-4-217 https://doaj.org/article/606311e758174aafa2d5fbb4c1b40497 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
BMC Research Notes, Vol 4, Iss 1, p 217 (2011) |
op_relation |
http://www.biomedcentral.com/1756-0500/4/217 https://doaj.org/toc/1756-0500 doi:10.1186/1756-0500-4-217 1756-0500 https://doaj.org/article/606311e758174aafa2d5fbb4c1b40497 |
op_doi |
https://doi.org/10.1186/1756-0500-4-217 |
container_title |
BMC Research Notes |
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4 |
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1 |
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1766362554261569536 |