title: Comparative transcriptional analysis of embryoid body versus two-dimensional differentiation of murine embryonic stem cells.
abstract: Understanding the process of ex vivo embryonic stem (ES) cell differentiation is important for generating higher yields of desirable cell types or lineages and for understanding fundamental aspects of ES differentiation. We used DNA microarray analysis to investigate the differentiation of mouse ES cells cultured under three differentiation conditions. Embryoid body (EB) formation was compared to differentiation on surfaces coated with either gelatin (GEL) or matrigel (MAT). Based on the transcriptional patterns of a list of literature-based "stemness" genes, ES cell differentiation on the two coated surfaces appeared similar but not identical to EB differentiation. A notable difference was the GEL and MAT upregulation but EB downregulation of nine such stemness genes, which are related to cell adhesion and epithelial differentiation. Further, GEL and MAT differentiation showed higher expression of bone formation-related genes (Spp1, Csf1, Gsn, Bmp8b, Crlf1). Gene ontology analysis shows an increase in the expression of genes related to migration and cell structure in all three conditions. Overall, GEL and MAT conditions resulted in a more similar to each other transcriptional profile than to the EB condition, and such differences are apparently related to higher nutrient and metabolite gradients and limitations in the EB versus the GEL or MAT cultures.
authors.affiliation: Department of Chemical Engineering and Biotechnology, Centre for Biochemical Engineering and Biotechnology, Institute for Cell Dynamics and Biotechnology (ICDB), University of Chile, Santiago, Chile.
authors.forename: Dario E
authors.initials: DE
authors.lastname: Sepulveda
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Andrews
authors.forename: Juan A
authors.initials: JA
authors.lastname: Asenjo
authors.forename: Eleftherios Terry
authors.initials: ET
authors.lastname: Papoutsakis
mesh_terms: D000704:Analysis of Variance; D000818:Animals; D019485:Bone Morphogenetic Proteins / Q000235:genetics; D018929:Cell Culture Techniques / Q000379:methods; D002454:Cell Differentiation / Q000235:genetics*; D003094:Collagen / Q000494:pharmacology; D004338:Drug Combinations; D053595:Embryonic Stem Cells / Q000166:cytology / Q000187:drug effects / Q000378:metabolism*; D005434:Flow Cytometry; D005780:Gelatin / Q000494:pharmacology; D018507:Gene Expression Regulation, Developmental / Q000187:drug effects; D007797:Laminin / Q000494:pharmacology; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D053495:Osteopontin / Q000235:genetics; D011509:Proteoglycans / Q000494:pharmacology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D014158:Transcription, Genetic
chemical_list: C415983:Bmp8b protein, mouse; D019485:Bone Morphogenetic Proteins; D004338:Drug Combinations; D007797:Laminin; D011509:Proteoglycans; C506896:Spp1 protein, mouse; D053495:Osteopontin; C059485:matrigel; D005780:Gelatin; D003094:Collagen