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Open Access Highly Accessed Methodology article

Efficient recovery of whole blood RNA - a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species

Doreen Schwochow12*, Laurel EK Serieys1, Robert K Wayne1 and Olaf Thalmann13

Author Affiliations

1 Department of Ecology and Evolutionary Biology, University of California Los Angeles, 2149 Terasaki Life Science Building, Los Angeles, 90095, USA

2 Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, BMC Husargatan 3, Uppsala, SE75124, Sweden

3 Division of Genetics and Physiology, Department of Biology, University of Turku, Iltäinen Pitkäkatu 4, Turku, 520014, Finland

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BMC Biotechnology 2012, 12:33  doi:10.1186/1472-6750-12-33

Published: 27 June 2012

Abstract

Background

Since the emergence of next generation sequencing platforms, unprecedented opportunities have arisen in the study of natural vertebrate populations. In particular, insights into the genetic and epigenetic mechanisms of adaptation can be revealed through study of the expression profiles of genes. However, as a pre-requisite to expression profiling, care must be taken in RNA preparation as factors like DNA contamination, RNA integrity or transcript abundance can affect downstream applications. Here, we evaluated five commonly used RNA extraction methods using whole blood sampled under varying conditions from 20 wild carnivores.

Results

Despite the use of minute starting volumes, all methods produced quantifiable RNA extracts (1.4 – 18.4 μg) with varying integrity (RIN 4.6 - 7.7), the latter being significantly affected by the storage and extraction method used. We observed a significant overall effect of the extraction method on DNA contamination. One particular extraction method, the LeukoLOCK™ filter system, yielded high RNA integrity along with low DNA contamination and efficient depletion of hemoglobin transcripts highly abundant in whole blood. In a proof of concept sequencing experiment, we found globin RNA transcripts to occupy up to ¼ of all sequencing reads if libraries were not depleted of hemoglobin prior to sequencing.

Conclusion

By carefully choosing the appropriate RNA extraction method, whole blood can become a valuable source for high-throughput applications like expression arrays or transcriptome sequencing from natural populations. Additionally, candidate genes showing signs of selection could subsequently be genotyped in large population samples using whole blood as a source for RNA without harming individuals from rare or endangered species.

Keywords:
Whole blood; RNA preservation; RNA extraction; DNA contamination; Transcriptome sequencing; Globin transcripts