Open Access Highly Accessed Technical Note

RNA isolation method for single embryo transcriptome analysis in zebrafish

Mark de Jong1, Han Rauwerda1, Oskar Bruning1, Jurgo Verkooijen1, Herman P Spaink2 and Timo M Breit1*

Author Affiliations

1 MicroArray Department & Integrative Bioinformatics Unit, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands

2 Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Einsteinweg 55, 2333 CE, Leiden, the Netherlands

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BMC Research Notes 2010, 3:73  doi:10.1186/1756-0500-3-73

Published: 16 March 2010



Transcriptome analysis during embryogenesis usually requires pooling of embryos to obtain sufficient RNA. Hence, the measured levels of gene-expression represent the average mRNA levels of pooled samples and the biological variation among individuals is confounded. This can irreversibly reduce the robustness, resolution, or expressiveness of the experiment. Therefore, we developed a robust method to isolate abundant high-quality RNA from individual embryos to perform single embryo transcriptome analyses using zebrafish as a model organism. Available methods for embryonic zebrafish RNA isolation minimally utilize ten embryos. Further downscaling of these methods to one embryo is practically not feasible.


We developed a single embryo RNA extraction method based on sample homogenization in liquid nitrogen, RNA extraction with phenol and column purification. Evaluation of this method showed that: the quality of the RNA was very good with an average RIN value of 8.3-8.9; the yield was always ≥ 200 ng RNA per embryo; the method was applicable to all stages of zebrafish embryogenesis; the success rate was almost 100%; and the extracted RNA performed excellent in microarray experiments in that the technical variation was much lower than the biological variation.


Presented is a high-quality, robust RNA isolation method. Obtaining sufficient RNA from single embryos eliminates the necessity of sample pooling and its associated drawbacks. Although our RNA isolation method has been setup for transcriptome analysis in zebrafish, it can also be used for other model systems and other applications like (q)PCR and transcriptome sequencing.