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MEF marker genes
Marker genes of feeder cells were identified using unpublished RNA-seq data provided by Dr Jafar Sharif and Dr Kyoichi Isono. Gene expression differences among ESCs, TSCs and MEFs were compared using the cuffdiff program, and genes that were significantly highly expressed in MEFs were selected. Genes encoding cytokines and extracellular matrix-related genes were selected to illustrate the features of feeder cells in Fig. 2E.
I would like to acknowledge Dr Akihiko Yoshimura, Keio University, who initially suggested on his website that NGS data could be evaluated by SNP analysis. Dr Ichiro Taniuchi and Dr Nyambayar Dashtsoodol, RIKEN-IMS, offered insightful information for interpreting the experimental procedures. Dr Norihito Hayatsu, RIKEN-IMS, provided unpublished inbred/outbred mice sequences to validate the genotype analysis. Dr Jafar Sharif and Dr Kyoichi Isono, RIKEN-IMS, provided unpublished transcriptome data to identify marker genes. Dr Shinichi Nakagawa, RIKEN, provided critical comments on my manuscript, and Mr David Gifford, RIKEN-CSRS, edited the text. I especially thank the authors of the retracted paper, Dr Teruhiko Wakayama, University of Yamanashi and Dr Hitoshi Niwa, RIKEN-CDB, for commenting on this manuscript.
Ben-David, U., Mayshar, Y. & Benvenisty, N. (2013) Virtual karyotyping of pluripotent stem cells on the basis of their global gene expression profiles. Nat. Protoc. 8, 989–997.
Chang, G., Gao, S., Hou, X. et al. (2014) High-throughput sequencing reveals the disruption of methylation of imprinted gene in induced pluripotent stem cells. Cell Res. 24, 293–306.
DeVeale, B., van der Kooy, D. & Babak, T. (2012) Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PLoS Genet. 8, e1002600.
Gropp, A. (1982) Value of an animal model for trisomy. Virchows Arch. A Pathol. Anat. Histol. 395, 117–131.
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Hussein, S.M., Batada, N.N., Vuoristo, S. et al. (2011) Copy number variation and selection during reprogramming to pluripotency. Nature 471, 58–62.
Kim, Y.M., Lee, J., Xia, L., Mulvihill, J.J. & Li, S. (2013) Trisomy 8: a common finding in mouse embryonic stem (ES) cell lines. Mol. Cytogenet. 6, 3–7.
Lagarrigue, S., Martin, L., Hormozdiari, F., Roux, P.F., Pan, C., van Nas, A., Demeure, O., Cantor, R., Ghazalpour, A., Eskin, E. & Lusis, A.J. (2013) アnalysis of allele-specific expression in mouse liver by RNA-Seq: a comparison with cis-eQTL identified using genetic linkage. Genetics 195, 1157–1166.
Liu, X., Wu, H., Loring, J., Hormuzdi, S., Disteche, C.M., Bornstein, P. & Jaenisch, R. (1997) Trisomy eight in ES cells is a common potential problem in gene targeting and interferes with germ line transmission. Dev. Dyn. 209, 85–91.
Mayshar, Y., Ben-David, U., Lavon, N., Biancotti, J.C., Yakir, B., Clark, A.T., Plath, K., Lowry, W.E. & Benvenisty, N. (2010) Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell 7, 521–531.
(Filename) gtc12178-sup-0001-FigS1.pdf
(Format) application/PDF
(Size) 265K
(Description) Figure S1 Allele distributions from the RNA-seq data obtained for the cell lines reported in the Obokata et al. study. CD45+ cells (gray), ESCs (yellow), STAP cells (blue), STAP-SCs (green), TSCs (orange), EpiSCs (light blue), and FI-SCs (red). The ESCs, STAP cells, STAP-SCs, FI-SCs, and epiblast stem cells (EpiSCs) were annotated as being derived from a 129B6F1 strain, and the TSCs as from a CD1 strain.
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(Filename) gtc12178-sup-0002-FigS2.pdf
(Format) application/PDF
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(Description) Figure S2 Allele frequencies of all chromosomes. SNPs on all autosomes and the X chromosome were counted, and their distributions are indicated. The RNA-seq data from the CD45+ and STAP cells are identical to those used in Fig. 3. Numbers after each chromosome name are those of applied SNPs of CD45+ rep1, CD45+ rep2, STAP rep1, and STAP rep2, respectively.
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(Filename) gtc12178-sup-0003-TableS1.xlsx
(Format) application/msexcel
(Size) 11K
(Description) Table S1 RNA-seq raw data used in this study
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