Additional Supporting Information may be found in the online version of this article.

sc-12-0645_sm_SupplFigure1a.tif2551KSupplement Figure 1. An example of a stable karyotypic change in the CCTL14 line visualized using G banding analysis (panel A) and the detail of chromosome change (panel B). Passaging intervals shortened with increasing passage number (panel C, upper graph) as a part of adaptation process. The average passaging interval for each window of 20 passages was plotted. A similar effect on passaging interval was observed for a second, independent cell line, CCTL12 (panel C, bottom graph).
sc-12-0645_sm_SupplFigure1b.tif1319KSupplement Figure 1b
sc-12-0645_sm_SupplFigure1c.tif2927KSupplement Figure 1c
sc-12-0645_sm_SupplFigure2.tif2546KSupplement Figure 2. Telomerase activity as measured by the telomerase reverse transcriptase (TERT) assay in cultured hESCs. The graph shows high and stable TERT activity at passages 32 to 366. The cultured hESCs have much higher TERT activity than both differentiated hESC-derived fibroblasts (hES-F) and embryonic bodies (EBs) derived from them, and than human foreskin fibroblasts (HFF) and mouse embryonic fibroblasts (MEFs). The experiments were done in triplicate, averaged and shown with corresponding standard error bars.
sc-12-0645_sm_SupplFigure3.tif2436KSupplement Figure 3. Level of NHEJ in hESC nuclear extracts from early medium and late passaged cells. Bars corresponding to the activity of hESC nuclear extracts are labeled according to the passage number of the cells from which the extracts were isolated. Extracts from hESC-derived fibroblasts (hES-Fs), recombinant T4 DNA ligase (Ligase) and sample with no extract added (BL) were included as controls. Activity is expressed as international units (IU). The experiments were done in triplicate, averaged and shown with corresponding standard error bars.
sc-12-0645_sm_SupplFigure4.pdf423KSupplement Figure 4. Immunohistochemical analysis of APE1 nuclear localization (green) in medium passage hESC line CCTL14. Cells were labeled with mitotracker to visualize mitochondria (red) and DAPI to visualize the nuclei (blue). A colony with heterogeneous expression of APE1 was chosen. White arrows show cells with high and low APE1 expression. No APE1 colocalization with mitochondria or cytosolic localization of APE1 was detected. 100x magnification was used to resolve mitochondria.
sc-12-0645_sm_SupplFigure5.tif1991KSupplement Figure 5. Immunohistochemical analysis of pluripotency markers in early and late passage hESC line CCTL14. No difference was detected in the level of pluripotency markers NANOG (red) and SSEA3 (green) between early and late passage cells. DAPI (blue) was used to visualize nuclei.
sc-12-0645_sm_SupplFigure6a.pdf440KSupplement Figure 6. Downregulation of APE1 protein after anti-APE1 siRNA transfection. hESCs were transfected with anti-APE1 siRNA, using X-tremeGene transfection reagent (siAPE1) or transfection reagent alone (X-treme). Cells were fixed and stained 1, 2, or 3 days after transfection (Day 1, Day 2, and Day 3) with anti-APE1 antibody (APE1) and DAPI nuclear staining (DAPI) (Panel A). The third column shows the merged images demonstrating APE1 localization. White bar on the bottom right represents the scale of 200 μm. APE1 protein was detected 3rd day after transfection in hESC CCTL14 by western blot analysis (panel B). Tubulin (Tu) was used as loading control. Expression of APE1 mRNA was analyzed 2nd and 3rd day after the transfection by qRT-PCR (panel C). Transcription levels were plotted relative to tubulin transcription.
sc-12-0645_sm_SupplFigure6b.tif1793KSupplement Figure 6b
sc-12-0645_sm_SupplFigure7a.tif1383KSupplement Figure 7. Proliferation and cell cycle parameters of hESC CCTL14 in early passage, late passage and early passage with downregulated APE1. Growth curve (panel 1) was measured after plating 103 cells for total of 91 hours. No difference between APE1 siRNA treated cells (siRNA) and corresponding control (Xtr). Cell cycle distribution of propidium iodide labeled early, late, APE siRNA treated (siRNA) and transfection control (Xtr) hESC CCTL14 was measured using flow cytometry (panel B). While no differences between early hESC, APE1 downregulated cells (siRNA) and corresponding control (Xtr) with strongest G1 phase were observed, more cells in S phase were observed in late passage hESC.
sc-12-0645_sm_SupplFigure7b.tif1728KSupplement Figure 7b
sc-12-0645_sm_SupplFigure8a.tif594KSupplement Figure 8. Downregulation of APE1 does not affect γ-H2AX foci formation in non-irradiated cells. Early passage hESCs were transfected with anti-APE1 siRNA (Si) or with transfection reagent alone (EXTR). Control cells of early passage (hESC) and late passage (LATE) were included. γ-H2AX foci were counted using ImageJ 42 and plotted (panel B). Values were for each of five experiments divided by corresponding value of early passage and ploted as relative values together with standard deviation as relative foci per nucleus (panel A). No significant differences were observed between cells with downregulated APE1 and controls. Immunohostochemical analysis of γ-H2AX foci within the course of 20 hours after induction of DNA damage by 3Gy of IR shows dynamics of foci formation and disappearance (panel C). Foci were counted using ImageJ image analysis and plotted (Panel D)
sc-12-0645_sm_SupplFigure8b.tif2820KSupplement Figure 8b
sc-12-0645_sm_SupplFigure8c.pdf100KSupplement Figure 8c
sc-12-0645_sm_SupplFigure8d.tif811KSupplement Figure 8d
sc-12-0645_sm_SupplFigure9a.tif1255KSupplement Figure 9. Analysis of apoptosis during the early events after DNA damage induction. Presence of apoptotic cells in hESC CCTL14 with downregulated APE1 (siRNA) and corresponding control (Control) was analyzed by TUNEL (green, panel A) for 6 hrs after inducing the DNA damage with 3Gy of IR. DAPI stained nuclei (blue) and phase contrast images of the cells (VIS) are included as control. PARP as an early marker of apoptosis was assayed by western blot (panel B). UV irradiated cells were included as positive control for PARP cleavage (PARP ctrl), tubuline (Tu) as loading control and APE1 as control of siRNA silencing. No change in apoptosis was detected in siRNA treated cells by either method.
sc-12-0645_sm_SupplFigure9b.tif778KSupplement Figure 9b
sc-12-0645_sm_SupplFigure10.pdf382KSupplement Figure 10. Methoxamine imhibits γ-H2AX signaling upon IR. Early passage hESC were irradiated with 3Gy after 30 min treatment with 40μM methoxamine. Cells were fixed 60 minutes after IR and stained for presence of phosphorylated histone γ-H2AX. Control cells were not treated with methoxamine. Methoxamine decreases the amount of cells containing γ-H2AX foci in unirradiated (panel A) and number of γ-H2AX foci in irradiated cells (Panel B).
sc-12-0645_sm_SupplFigureLegends.pdf25KSupplement Figure Legends

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