Cardiac Embryology and Reconstructions

Leader: Jan Ruijter


In previous years my group has developed methods for 3D analysis and visualization of gene expression patterns and morphogenetic parameters during embryogenesis as well as for the analysis of quantitative PCR (LinRegPCR) and transcript count (SAGEstat and Gtest) data. The computer programs resulting from this work were made available and are frequently cited and downloaded. In the field of cardiac development we have implemented new methods for analysis and visualization of morphogenetic parameters and gene expression patterns in 3D-space, which have taken a prominent place in the papers of the research lines of the department. In the EU-funded CHeartED project, my group has created a database of 3D gene expression to genetically annotate and identify components of the developing heart. In the EU-funded CardioNeT project, the methods for 3D measurement of growth and differentiation of the heart are being applied to study the role of regulators of development in normal and abnormal cardiac growth. In the NHS-funded COBRA3 project we will extend this quantitative analysis of cardiac growth to the post-natal period to study the long-term effect of the challenge that cardiac malformations put onto the maintenance of cardiac homeostasis. Cluster analysis will be used to identify associations between gene expression patterns and cardiac components and to compare the role of morphogenetic parameters in normal and abnormal cardiac development. Mouse lines that display transgenic lineage markers will be included to trace the cellular and developmental origin of the different cardiac compartments. Furthermore, I will further develop and update the LinRegPCR program for analysis of qPCR data. The introduction of Deep-SAGE, using mRNA sequencing, has renewed the interest in comparison and statistical analysis of transcript counts, requiring further development of the Gtest program. Additionally, my group developed OccuPeak for analysis of ChP-seq data that are generated in cardiac development and arrhythmia projects and is currently working on a method to combine peak sets resulting from different ChIP-seq datasets.

Team members

Jan RuijterGroup Leader (PI)
Antoon MoormanScientific Advisor
Jaco HagoortSystem- and data analyst
Bernadette de BakkerPhD student
Karel van DuijvenbodenPhD student
Stuti PrakashPhD student
Nora ChekrouniStudent
Robel MichaelStudent
Ward van der VenStudent

Key publications

de Boer B. A., van Duijvenboden K., van den Boogaa et al., PLoS.ONE., 2014 
Ruijter J. M., Pfaffl M. W., Zhao S., et al. et al., Methods, 2012 
de Boer B. A., van den Berg G., de Boer P. A., et et al., Dev Biol., 2012 
de Bakker B. S., de Jong K. H., Hagoort J., et al. et al., Reprod.Toxicol., 2012 
de Boer B. A., Soufan A. T., Hagoort J., et al. et al., Development, 2011 
Ruijter J. M., Ramakers C., Hoogaars W. M., et al. et al., Nucleic Acids Res., 2009 
Soufan A. T., van den Berg G., Moerland P. D., et et al., J Microsc, 2007 

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