Author Posting. © The Author(s), 2010. This is the author's version of the work. It is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Eukaryotic Cell 9 (2010): 1566-1576, doi:10.1128/EC.00100-10. ; The protozoan parasite Giardia lamblia undergoes stage-differentiation in the small intestine of the host to an environmentally resistant and infectious cyst. Encystation involves secretion of an extracellular matrix comprised of cyst wall proteins (CWPs) and a β(1-3)-GalNAc homopolymer. Upon induction of encystation, genes coding for CWPs are switched on, and mRNAs coding for a transcription factor Myb and enzymes involved in cyst wall glycan synthesis are upregulated. Encystation in vitro is triggered by several protocols, which call for changes in bile concentrations or availability of lipids, and elevated pH. However, the conditions for induction are not standardized and we predicted significant protocol-specific side effects. This makes reliable identification of encystation factors difficult. Here, we exploited the possibility to induce encystation with two different protocols, which we show to be equally effective, for a comparative mRNA profile analysis. The standard encystation protocol induced a bipartite transcriptional response with surprisingly minor involvement of stress genes. A comparative analysis revealed a core set of only 18 encystation genes and showed that a majority of genes was indeed upregulated as a side effect of inducing conditions. We also established a Myb binding sequence as a signature motif in encystation promoters, suggesting coordinated regulation of these factors. ; We acknowledge in particular the “Stiftung zur Förderung der Wissenschaftlichen Forschung an der Universität Zürich” for financial support for this project. C.S. was supported by the Roche and Novartis Foundation, and “Stiftung für Forschungsförderung” University of Zurich. Research in the Hehl laboratory is supported by the Swiss National Science Foundation (grant #31003A-125389).