Aryee, M.J., Jaffe, A.E., Corrada-Bravo, H., Ladd-Acosta, C., Feinberg, A.P., Hansen, K.D., and Irizarry, R.A. (2014). Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microar- rays. Bioinformatics 30, 1363–1369.
Balaton, B.P., Cotton, A.M., and Brown, C.J. (2015). Derivation of consensus inactivation status for X-linked genes from genome-wide studies. Biol. Sex Differ. 6, 35.
Ban, H., Nishishita, N., Fusaki, N., Tabata, T., Saeki, K., Shikamura, M., Ta- kada, N., Inoue, M., Hasegawa, M., Kawamata, S., and Nishikawa, S.I. (2011). Efficient generation of transgene-free human induced pluripotent stem cells (iPSCs) by temperature-sensitive Sendai virus vectors. Proc. Natl. Acad. Sci. USA 108, 14234–14239.
Ben-David, U., and Benvenisty, N. (2011). The tumorigenicity of human embry- onic and induced pluripotent stem cells. Nat. Rev. Cancer 11, 268–277.
Bock, C., Kiskinis, E., Verstappen, G., Gu, H., Boulting, G., Smith, Z.D., Ziller, M., Croft, G.F., Amoroso, M.W., Oakley, D.H., et al. (2011). Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell 144, 439–452.
Cahan, P., and Daley, G.Q. (2013). Origins and implications of pluripotent stem cell variability and heterogeneity. Nat. Rev. Mol. Cell Biol. 14, 357–368.
Di Stefano, B., Ueda, M., Sabri, S., Brumbaugh, J., Huebner, A.J., Sahakyan, A., Clement, K., Clowers, K.J., Erickson, A.R., Shioda, K., et al. (2018). Reduced MNAI¨VEhibition preserves genomic stability in naive human embry-onic stem cells. Nat. Methods 15, 732–740.
Dobin, A., Davis, C.A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., and Gingeras, T.R. (2013). STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21.
Fusaki, N., Ban, H., Nishiyama, A., Saeki, K., and Hasegawa, M. (2009). Effi- cient induction of transgene-free human pluripotent stem cells using a vector based on Sendai virus, an RNA virus that does not integrate into the host genome. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 85, 348–362.
Gogarten, S.M., Bhangale, T., Conomos, M.P., Laurie, C.A., McHugh, C.P., Painter, I., Zheng, X., Crosslin, D.R., Levine, D., Lumley, T., et al. (2012). GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies. Bioinformatics 28, 3329–3331.
Gonza´ lez, J.R., Rodrı´guez-Santiago, B., Ca´ ceres, A., Pique-Regi, R., Roth- man, N., Chanock, S.J., Armengol, L., and Pe´ rez-Jurado, L.A. (2011). A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data. BMC Bioinf. 12, 166.
Guo, G., von Meyenn, F., Rostovskaya, M., Clarke, J., Dietmann, S., Baker, D., Sahakyan, A., Myers, S., Bertone, P., Reik, W., et al. (2017). Epigenetic reset- ting of human pluripotency. Development 144, 2748–2763.
Inoue, M., Tokusumi, Y., Ban, H., Kanaya, T., Tokusumi, T., Nagai, Y., Iida, A., and Hasegawa, M. (2003). Nontransmissible virus-like particle formation by F-deficient sendai virus is temperature sensitive and reduced by mutations in M and HN proteins. J. Virol. 77, 3238–3246.
Io, S., Kabata, M., Iemura, Y., Semi, K., Morone, N., Minagawa, A., Wang, B., Okamoto, I., Nakamura, T., Kojima, Y., et al. (2021). Capturing human tropho- blast development with naive pluripotent stem cells in vitro. Cell Stem Cell 28, 1023–1039.e13.
Kilens, S., Meistermann, D., Moreno, D., Chariau, C., Gaignerie, A., Reignier, A., Lelie` vre, Y., Casanova, M., Vallot, C., Nedellec, S., et al. (2018). Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. Nat. Commun. 9, 360.
Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F.P., Culley, O.J., et al. (2017). Common genetic vari- ation drives molecular heterogeneity in human iPSCs. Nature 546, 370–375.
Komuta, Y., Ishii, T., Kaneda, M., Ueda, Y., Miyamoto, K., Toyoda, M., Ume- zawa, A., and Seko, Y. (2016). In vitro transdifferentiation of human peripheral blood mononuclear cells to photoreceptor-like cells. Biol. Open 5, 709–719.
Kobayashi, T., Yamaguchi, T., Hamanaka, S., Kato-Itoh, M., Yamazaki, Y., Ibata, M., Sato, H., Lee, Y.S., Usui, J.I., Knisely, A.S., et al. (2010). Generation of rat pancreas in mouse by interspecific blastocyst injection of pluripotent stem cells. Cell 142, 787–799.
Kondo, H., and Yonezawa, Y. (1995). Fetal-adult phenotype transition, in terms of the serum dependency and growth factor requirements, of human skin fibroblast migration. Exp. Cell Res. 220, 501–504.
Kono, K., Sawada, R., Kuroda, T., Yasuda, S., Matsuyama, S., Matsuyama, A., Mizuguchi, H., and Sato, Y. (2019). Development of selective cytotoxic viral vectors for concentration of undifferentiated cells in cardiomyocytes derived from human induced pluripotent stem cells. Sci. Rep. 9, 3630.
Li, B., and Dewey, C.N. (2011). RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 12, 323.
Li, H.O., Zhu, Y.F., Asakawa, M., Kuma, H., Hirata, T., Ueda, Y., Lee, Y.S., Fu- kumura, M., Iida, A., Kato, A., et al. (2000). A cytoplasmic RNA vector derived from nontransmissible Sendai virus with efficient gene transfer and expres- sion. J. Virol. 74, 6564–6569.
Liao, Y., Smyth, G.K., and Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinfor- matics 30, 923–930.
Liu, X., Nefzger, C.M., Rossello, F.J., Chen, J., Knaupp, A.S., Firas, J., Ford, E., Pflueger, J., Paynter, J.M., Chy, H.S., et al. (2017). Comprehensive character- ization of distinct states of human naive pluripotency generated by reprogram- ming. Nat. Methods 14, 1055–1062.
Liu, X., Tan, J.P., Schro¨ der, J., Aberkane, A., Ouyang, J.F., Mohenska, M., Lim, S.M., Sun, Y.B.Y., Chen, J., Sun, G., et al. (2021). Modelling human blastocysts by reprogramming fibroblasts into iBlastoids. Nature 591, 627–632.
Madrid, M., Sumen, C., Aivio, S., and Saklayen, N. (2021). Autologous induced pluripotent stem cell-based cell therapies: promise, progress, and challenges. Curr. Protoc. 1, e88.
Nakagawa, M., Koyanagi, M., Tanabe, K., Takahashi, K., Ichisaka, T., Aoi, T., Okita, K., Mochiduki, Y., Takizawa, N., and Yamanaka, S. (2008). Generation of induced pluripotent stem cells without Myc from mouse and human fibro- blasts. Nat. Biotechnol. 26, 101–106.
Nakagawa, M., Takizawa, N., Narita, M., Ichisaka, T., and Yamanaka, S. (2010). Promotion of direct reprogramming by transformation-deficient Myc. Proc. Natl. Acad. Sci. USA 107, 14152–14157.
Nichols, J., and Smith, A. (2009). Naive and primed pluripotent states. Cell Stem Cell 4, 487–492.
Okita, K., Ichisaka, T., and Yamanaka, S. (2007). Generation of germline- competent induced pluripotent stem cells. Nature 448, 313–317.
Pastor, W.A., Chen, D., Liu, W., Kim, R., Sahakyan, A., Lukianchikov, A., Plath, K., Jacobsen, S.E., and Clark, A.T. (2016). Naive human pluripotent cells feature a methylation landscape devoid of blastocyst or germline memory. Cell Stem Cell 18, 323–329.
Sahakyan, A., Kim, R., Chronis, C., Sabri, S., Bonora, G., Theunissen, T.W., Kuoy, E., Langerman, J., Clark, A.T., Jaenisch, R., and Plath, K. (2017). Human naive pluripotent stem cells model X chromosome dampening and X inactiva- tion. Cell Stem Cell 20, 87–101.
Schlaeger, T.M. (2018). Nonintegrating human somatic cell reprogramming methods. Adv. Biochem. Eng. Biotechnol. 163, 1–21.
Takahashi, K., Okita, K., Nakagawa, M., and Yamanaka, S. (2007). Induction of pluripotent stem cells from fibroblast cultures. Nat. Protoc. 2, 3081–3089.
Takashima, Y., Guo, G., Loos, R., Nichols, J., Ficz, G., Krueger, F., Oxley, D., Santos, F., Clarke, J., Mansfield, W., et al. (2014). Resetting transcription factor control circuitry toward ground-state pluripotency in human. Cell 158, 1254– 1269.
Theunissen, T.W., Friedli, M., He, Y., Planet, E., O’Neil, R.C., Markoulaki, S., Pontis, J., Wang, H., Iouranova, A., Imbeault, M., et al. (2016). Molecular criteria for defining the naive human pluripotent state. Cell Stem Cell 19, 502–515.
Theunissen, T.W., Powell, B.E., Wang, H., Mitalipova, M., Faddah, D.A., Reddy, J., Fan, Z.P., Maetzel, D., Ganz, K., Shi, L., et al. (2014). Systematic identification of culture conditions for induction and maintenance of naive hu- man pluripotency. Cell Stem Cell 15, 524–526.
Thomson, J.A., Itskovitz-Eldor, J., Shapiro, S.S., Waknitz, M.A., Swiergiel, J.J., Marshall, V.S., and Jones, J.M. (1998). Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147.
Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S.F.A., Hakonarson, H., and Bucan, M. (2007). PennCNV: an integrated hidden Markov model de- signed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 17, 1665–1674.
Weinberger, L., Ayyash, M., Novershtern, N., and Hanna, J.H. (2016). Dynamic stem cell states: naive to primed pluripotency in rodents and humans. Nat. Rev. Mol. Cell Biol. 17, 155–169.
Yamaguchi, T., Sato, H., Kato-Itoh, M., Goto, T., Hara, H., Sanbo, M., Mizuno, N., Kobayashi, T., Yanagida, A., Umino, A., et al. (2017). Interspecies organo- genesis generates autologous functional islets. Nature 542, 191–196.
Yan, L., Yang, M., Guo, H., Yang, L., Wu, J., Li, R., Liu, P., Lian, Y., Zheng, X., Yan, J., et al. (2013). Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat. Struct. Mol. Biol. 20, 1131–1139.
Yanagida, A., Spindlow, D., Nichols, J., Dattani, A., Smith, A., and Guo, G. (2021). Naive stem cell blastocyst model captures human embryo lineage segregation. Cell Stem Cell 28, 1016–1022.e4.
Yu, L., Wei, Y., Duan, J., Schmitz, D.A., Sakurai, M., Wang, L., Wang, K., Zhao, S., Hon, G.C., and Wu, J. (2021). Blastocyst-like structures generated from hu- man pluripotent stem cells. Nature 591, 620–626.
Zhang, Z., Hong, Y., Xiang, D., Zhu, P., Wu, E., Li, W., Mosenson, J., and Wu, W.S. (2015). MicroRNA-302/367 cluster governs hESC self-renewal by dually regulating cell cycle and apoptosis pathways. Stem Cell Rep. 4, 645–657.
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