Fig. 1

Cell line characterization and global analysis of DNA epigenetic modifications. a Representative immunofluorescence staining (IF) of PDX-derived glioma stem cell (GSC) line GSC12, labeled with the percent positive cells for each marker. Blue-DAPI, green-SOX-2, red-NESTIN, GFAP, and TUBB3. b Representative IF of a neural stem cell (NSC27) line, labeled as in (a). c Percent positive cells for each marker in the core set of GSCs by IF. X-axis denotes the cell line. Y-axis denotes the percent positive cells. d TET1, TET2, TET3, and TDG expression by quantitative reverse transcription polymerase chain reaction (qRT-PCR), normalized to DYNLL and expressed as the mean ± SEM. Dashed line marks the average expression level of each gene in NSCs. Boxplots depict the distribution of TET expression in NSC and GSC. X-axis denotes the cell line. Y-axis denotes the normalized messenger RNA (mRNA) expression. e Immunohistochemical quantification of 5mC and 5hmC at the margin of the tumor in PDX GBM6, GBM64, and GBM84 as indicated on top of the image. Images are enlarged to view the difference in staining intensity between tumor and surrounding normal murine tissue. f A heatmap of the correlation between the global level of DNA marks measured by mass spectrometry and expression of DNMTs and TETs. Blue: negative correlation; yellow: positive correlation. Asterisk – significant correlation with P < 0.05