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Fig. 9 | Genome Biology

Fig. 9

From: Distinctive epigenomes characterize glioma stem cells and their response to differentiation cues

Fig. 9

Co-expression of the TETs with DNA damage response genes and the functional impact of TET knockdown on cell viability under DNA damage conditions. a Transcript abundance for TET2 (far left) with the top four browser tracks displaying RNA-seq signals for GSC6, GSC12, GSC14, and GSC102, and the bottom two tracks showing RNA-seq data for NSC23 and NSC27. The three panels to the right show transcript levels (top four tracks, from RNA-seq) and 5fC/5caC levels (based on MAB-seq data, bottom four tracks) at the promoters of ABL1, RBM38, and TP73 in the indicated GSC and NSC lines. Order of cell lines is the same for RNA-seq data (top four tracks) and MAB-seq data (bottom four tracks). The genomic coordinates are denoted on the top of the track. Scale bar is indicated. Y-axis denotes the enrichment level represented by the raw reads of RNA-seq and ratio of modified reads to total reads for 5fC/5caC level. Red dashed box indicates the differentially modified promoter regions. b Venn diagrams showing the overlap of genes correlating with expression of each TET from the RNA-seq datasets. Left: positively correlated; right: negatively correlated. c Bar graphs showing ontology analysis of TET2 positively and negatively correlated genes. d Venn diagrams showing the overlap of genes correlating with expression of each TET in the TCGA GBM RNA-seq dataset. Top: positively correlated; bottom: negatively correlated. e Line graph showing the response of GSC6, GSC84, and NSC30 to bleomycin at different concentrations after 72 h. Data are normalized to the absorbance at 470 nm of vehicle and expressed as the mean ± SEM. Three replicates are performed for each drug concentration. Significance difference is assessed between each GSC and NSC30. *P < 0.05. **P < 0.01. f Line graph showing the viability of GSC6 transfected with each of the indicated small interfering RNAs at different concentrations of bleomycin and viability expressed as in part E. Significance difference is assessed between siNTC, siTET2, and siTET3. *P < 0.05. **P < 0.01. ns not significant

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