Comparison of five RNA extraction methods from rabbit’s blood

Nour, Afif M. Abdel; Barbour, Elie K.; Depint, Flore; Dooms, Maxime; Niang, Khadim; Dulac, Amélie; Niamba, Claude-Narcisse; Chaaya, Ghenwa; Pouillart, P.

doi:10.5251/abjna.2010.1.4.448.450

Cited by 6 publications

(3 citation statements)

References 10 publications

(9 reference statements)

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“…However, the relationship between the amount of sample and the RNA yield is not linear and each kit normally has an optimal range of sample concentration (PureLink™ - up to 1 × 10 9 bacteria, PureZOL™ - up to 2.4 × 10 9 bacteria, FastRNA ® Pro Blue- up to 1 × 10 9 bacteria). Nour et al [6] extracted RNA from rabbit blood samples using different extraction kits and determined that in one of the extraction kits used, too much concentrated sample would result in lower yield. However, in the majority of the cases reported, a lower initial sample concentration, yields lower amounts of RNA [6].…”

Section: Resultsmentioning

confidence: 99%

“…Nour et al [6] extracted RNA from rabbit blood samples using different extraction kits and determined that in one of the extraction kits used, too much concentrated sample would result in lower yield. However, in the majority of the cases reported, a lower initial sample concentration, yields lower amounts of RNA [6]. In the specific case of biofilms, higher cell densities will also mean higher external protein and polysaccharide contents, as confirmed herein (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

“…The success of any RNA-based analysis depends on the yield, purity, and integrity of the RNA [4,5]. However, different RNA extraction methods can yield RNA with varying levels of quality [6,7]. Currently, there are numerous methods for RNA extraction available, however there are only a few published studies comparing RNA extraction from biofilm samples [8-10].…”

Section: Introductionmentioning

confidence: 99%

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Comparison of RNA extraction methods from biofilm samples of Staphylococcus epidermidis

2011

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BackgroundMicrobial biofilms are communities of bacteria adhered to a surface and surrounded by an extracellular polymeric matrix. Biofilms have been associated with increased antibiotic resistance and tolerance to the immune system. Staphylococcus epidermidis is the major bacterial species found in biofilm-related infections on indwelling medical devices. Obtaining high quality mRNA from biofilms is crucial to validate the transcriptional measurements associated with the switching to the biofilm mode of growth. Therefore, we selected three commercially available RNA extraction kits with distinct characteristics, including those using silica membrane or organic extraction methods, and enzymatic or mechanical cell lysis, and evaluated the RNA quality obtained from two distinct S. epidermidis bacterial biofilms.ResultsRNA extracted using the different kits was evaluated for quantity, purity, integrity, and functionally. All kits were able to extract intact and functional total RNA from the biofilms generated from each S. epidermidis strain. The results demonstrated that the kit based on mechanical lysis and organic extraction (FastRNA® Pro Blue) was the only one that was able to isolate pure and large quantities of RNA. Normalized expression of the icaA virulence gene showed that RNA extracted with PureLink™ had a significant lower concentration of icaA mRNA transcripts than the other kits tested.ConclusionsWhen working with complex samples, such as biofilms, that contain a high content extracellular polysaccharide and proteins, special care should be taken when selecting the appropriate RNA extraction system, in order to obtain accurate, reproducible, and biologically significant results. Among the RNA extraction kits tested, FastRNA® Pro Blue was the best option for both S. epidermidis biofilms used.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Comparison of RNA extraction methods from biofilm samples of Staphylococcus epidermidis

2011

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Variability of RNA Quality Extracted from Biofilms of Foodborne Pathogens Using Different Kits Impacts mRNA Quantification by qPCR

2012

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The biofilm formation by foodborne pathogens is known to increase the problem related with surface disinfection procedure in the food processing environment and consequent transmission of these pathogens into the population. Messenger RNA has been increasingly used to understand the action and the consequences of disinfectants in the virulence on such biofilms. RNA quality is an important requirement for any RNA-based analysis since the quality can impair the mRNA quantification. Therefore, we evaluated five different RNA extraction kits using biofilms of the foodborne pathogens Listeria monocytogenes, Escherichia coli, and Salmonella enterica. The five kits yielded RNA with different quantities and qualities. While for E. coli the variability of RNA quality did not affect the quantification of mRNA, the same was not true for L. monocytogenes or S. enterica. Therefore, our results indicate that not all kits are suitable for RNA extraction from bacterial biofilms, and thus, the selection of RNA extraction kit is crucial to obtain accurate and meaningful mRNA quantification.

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Evaluation of different RNA extraction methods for high-quality total RNA and mRNA from Erwinia amylovora in planta

et al. 2016

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Obtaining a sufficient quantity of high-quality, intact RNA is the first crucial step in its study by RNA sequencing on next-generation sequencing platforms or quantitative PCR. Different RNA extraction methods or commercial kits vary in yield and in the quality and integrity of the RNA obtained, which may affect the results of downstream applications. Often, these factors depend on the organism under study and nature of the sample. Therefore, the selection of an appropriate RNA isolation method is critical. In this study, we present the results of an evaluation of three different commercial kits for the isolation of total RNA from Erwinia amylovora in apple tissue as well as the usefulness of different kinds of Deoxyribonuclease I for DNA removal and kits for rRNA depletion. To our knowledge, this is the first report on the method of isolation of high-quality E.amylovora mRNA for RNA-seq.

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Comparison of five RNA extraction methods from rabbit’s blood

Cited by 6 publications

References 10 publications

Comparison of RNA extraction methods from biofilm samples of Staphylococcus epidermidis

Comparison of RNA extraction methods from biofilm samples of Staphylococcus epidermidis

Variability of RNA Quality Extracted from Biofilms of Foodborne Pathogens Using Different Kits Impacts mRNA Quantification by qPCR

Evaluation of different RNA extraction methods for high-quality total RNA and mRNA from Erwinia amylovora in planta

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