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STEM_617_sm_suppinfoFigureS1.jpg419KFigure S1. In vitro differentiation of 129R3 for 6 days, where most of the cells appear to have a Giant cell like status (left). RT-PCR of several trophoblast cell marker genes illustrating that 129R3 cells differentiate into many trophoblast cell types. D2, D4 and D6 indicate differentiation for 2, 4 or 6 days.
STEM_617_sm_suppinfoFigureS2.jpg342KFigure S2. 129R3 chimeras were collected at 12.5 dpc (top) and 18.5 dpc (middle). Embryo or placenta DNA was extracted separately. Genotyping by PCR revealed that placentas, not embryos, were positive for the rtTA sequence, which indicates the existence of 129R3 (bottom).
STEM_617_sm_suppinfoFigureS3.jpg444KFigure S3. RT-PCR result showing overexpression of specific exogenous reprogramming factors after adding doxycycline for 3 days (top). The kinetics and reprogramming efficiency of different combinations of reprogramming factors were not alike, as indicated in the table (bottom).
STEM_617_sm_suppinfoFigureS4.jpg3144KFigure S4. Reprogramming of a TS cell line derived from OG2rtTA embryo into pluripotent stem cells by Oct4. A-A'. An Oct4-GFP positive colony appeared from the Oct4-induced TS cells derived from OG2rtTA embryo. B-B'. Early passage of the Oct4-induced pluripotent stem cells derived from OG3rtTA TS cells.
STEM_617_sm_suppinfoFigureS5.jpg1215KFigure S5. OiPS and 4F iPS cells both stained positive for alkaline phosphatase.
STEM_617_sm_suppinfoFigureS6.jpg241KFigure S6 RT-PCR results indicate that the expression of exogeneous genes was silenced in iPS cells after doxcycline withdraw.
STEM_617_sm_suppinfoFigureS7.jpg274KFigure S7. Karyotype of OiPS and 4F iPS cells was normal: 40, XX.
STEM_617_sm_suppinfoFigureS8.jpg242KFigure S8. Quantitative PCR showed that the endogenous expression of Oct4, Sox2, Klf4, c-Myc and Nanog in OiPS and 4F iPS cells was comparable to R1 ES cells, while Cdx2 expression could only be detected in 129R3 TS cells. The Y-axis represents fold expression relative to R1.
STEM_617_sm_suppinfoFigureS9.jpg670KFigure S9. Microarray data comparing gene expression in OiPS, 4F iPSR1 and 129R3 cells. A. Expression of ES cell marker genes indicates that OiPS and 4F iPS cells express many of the pluripotent genes expressed in R1. B. X-chromosome related genes expressed much higher in OiPS cells than 4F iPS and R1 cells. C. Imprinted genes IGF2/H19 are more highly expressed, in iPS cells than in R1 cells, but imprinted genes Peg5 and Peg10 have lower expression levels in iPS cells than in R1 cells. The Y-axis represents fold expression relative to R1.
STEM_617_sm_suppinfoFigureS10.jpg337KFigure S10. A. A histogram generated from the microarray data indicates that several X-chromosome genes are more highly expressed in OiPS and 4F iPS cells than in R1 ES cells. B. A histogram generated from the microarray data indicates that Y-chromosome genes only have background levels of expression in OiPS and 4F iPS cells, whereas Y-chromosome gene expression was much higher in R1 ES cells. C. A Histogram generated from the microarray data showing the expression profile from the imprinted Gtl2 family genes. Gtl2 and Rian are expressed at lower levels in OiPS and 4F iPS cells, whereas Dlk1 and Dio3 are expressed at levels comparable to R1 ES cell levels. The Y-axis represents fold expression relative to R1.
STEM_617_sm_suppinfoFigureS11.jpg4174KFigure S11. In vitro differentiation of OiPS and 4F iPS cells at Day 4 of EB (top) and after being plated for 7 days (middle). Quantitative RT-PCR results indicate that marker genes from the three germ layers are highly expressed in differentiated cells (OiPS-8 D and 4F iPS-4 D).

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