Expression profiling of 6 huES cell lines. (A) RT-PCR analysis of 6 ES cell lines showed consistent expression of markers of undifferentiated cells. PES cells are a pooled sample of 3 huES cell lines (GE01, GE07, and GE09). G3PDH served as an internal control. (B) Scatter plot analysis of cy5- and cy3-labeled genes in BG02 huES cells and huURNA sample indicating differential gene expression. Some significantly overexpressed ES cell genes are listed. (C) Hierarchical clustering of genes that were expressed 3-fold or at a higher level compared with huURNA. The color indicates the relative expression levels of each gene, with red indicating higher expression, green indicating negative expression, and black representing absent expression. The 5 genes as indicated by the arrows were not present in all cell lines. The minimum spot intensity for all genes was set at 150 fluorescence units except for the CER1 and DNMT3B genes; the minimum intensity was set at 100 fluorescence units for this analysis only to compare expression with other genes within the same array.