Comprehensive gene expression analysis of Bruce-4 embryonic stem cells by SAGE

Mouse embryonic stem cells lines derived from different mouse strains show considerable variation concerning their culture conditions, gene targeting efficiency and germ line transmission capacity. To gain insight into the basis for this phenomenon, we generated a SAGE library of the C57BL/6 derived ES cell line Bruce-4 and compared their gene expression to 129 strain-derived cells, which in general show the best performance in gene targeting experiments. Gene Ontology (GO) analyses for functional groups of genes demonstrated considerably higher expression of clusters indicating cellular differentiation as well as cell-cell and cell-matrix adhesion in R1 than in Bruce-4 cells. At the single gene level, almost 90% of the most strongly expressed transcripts in each library were significantly differential. Regarding transcripts that have been linked to stem cell state, seven of the 20 selected genes were expressed in both cell lines, eleven showed stronger expression in Bruce-4 ES cells and only one in R1 cells. These results suggest that expression of “stemness” genes cannot be used as a sole criterion for efficiency of ES cells in gene targeting experiments. Keywords: Embryonic stem cells, SAGE, gene expression profile We generated a SAGE library of the C57BL/6-derived ES cell line Bruce-4 and compared their gene expression to an already available SAGE library of 129-derived R1 ES cells generated by Anisimov et al (GSM72878).