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Open Access Research article

Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate

Nicole A Datson1*, Maarten C Morsink1, Srebrena Atanasova2, Victor W Armstrong2, Hans Zischler3, Christina Schlumbohm4, Bas E Dutilh5, Martijn A Huynen5, Brigitte Waegele6, Andreas Ruepp6, E Ronald de Kloet1 and Eberhard Fuchs4

Author Affiliations

1 Division of Medical Pharmacology, Leiden/Amsterdam Center for Drug Research and Leiden University Medical Center, The Netherlands

2 Department of Clinical Chemistry, Georg-August University, Goettingen, Germany

3 Institute of Anthropology, University of Mainz, Mainz, Germany

4 Clinical Neurobiology Laboratory, German Primate Center, Göttingen, Germany

5 Center for Molecular and Biomolecular Informatics/Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA, Nijmegen, The Netherlands

6 Institute for Bioinformatics, GSF – National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, Germany

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BMC Genomics 2007, 8:190  doi:10.1186/1471-2164-8-190

Published: 25 June 2007

Abstract

Background

The common marmoset monkey (Callithrix jacchus), a small non-endangered New World primate native to eastern Brazil, is becoming increasingly used as a non-human primate model in biomedical research, drug development and safety assessment. In contrast to the growing interest for the marmoset as an animal model, the molecular tools for genetic analysis are extremely limited.

Results

Here we report the development of the first marmoset-specific oligonucleotide microarray (EUMAMA) containing probe sets targeting 1541 different marmoset transcripts expressed in hippocampus. These 1541 transcripts represent a wide variety of different functional gene classes. Hybridisation of the marmoset microarray with labelled RNA from hippocampus, cortex and a panel of 7 different peripheral tissues resulted in high detection rates of 85% in the neuronal tissues and on average 70% in the non-neuronal tissues. The expression profiles of the 2 neuronal tissues, hippocampus and cortex, were highly similar, as indicated by a correlation coefficient of 0.96. Several transcripts with a tissue-specific pattern of expression were identified. Besides the marmoset microarray we have generated 3215 ESTs derived from marmoset hippocampus, which have been annotated and submitted to GenBank [GenBank: EF214838EF215447, EH380242EH382846].

Conclusion

We have generated the first marmoset-specific DNA microarray and demonstrated its use to characterise large-scale gene expression profiles of hippocampus but also of other neuronal and non-neuronal tissues. In addition, we have generated a large collection of ESTs of marmoset origin, which are now available in the public domain. These new tools will facilitate molecular genetic research into this non-human primate animal model.