DBTMEE: A database of transcriptome in mouse early embryos

Nucleic Acids Research

Volumn 43, Issue D1, 2015, Pages D771-D776

  Park, Sung Joon ^a   Shirahige, Katsuhiko ^a   Ohsugi, Miho ^a   Nakai, Kenta ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTOME; HISTONE;

ACCESS TO INFORMATION; ARTICLE; CELL DIFFERENTIATION; COMPUTER INTERFACE; COMPUTER SYSTEM; EMBRYO; EMBRYO DEVELOPMENT; EPIGENETICS; GENE EXPRESSION PROFILING; GENETIC DATABASE; MOUSE; NONHUMAN; ONLINE SYSTEM; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; REPRODUCIBILITY; VALIDATION PROCESS; ANIMAL; ANIMAL EMBRYO; EMBRYOLOGY; GENETICS; INTERNET; METABOLISM;

ANIMALS; DATABASES, GENETIC; EMBRYO, MAMMALIAN; GENE EXPRESSION PROFILING; HISTONES; INTERNET; MICE;

EID: 84941087940     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1001     Document Type: Article

References (14)

1. Shultz, R. M. (2002) The molecular foundations of the maternal to zygotic transition in the preimplantation embryo. Hum. Reprod. Update, 8, 323-331.
2. Wang, H. and Dey, S. K. (2006) Roadmap to embryo implantation: clues from mouse models. Nat. Rev. Genet., 7, 185-199.
3. Kobayashi, H., Sakurai, T., Imai, M., Takahashi, N., Fukuda, A., Yayoi, O., Sato, S., Nakabayashi, K., Hata, K., Sotomaru, Y. et al. (2012) Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet., 8, e1002440.
4. Erkek, S., Hisano, M., Liang, C. Y., Gill, M., Murr, R., Dieker, J., Schubeler, D., Vlag, J. V., Stadler, M. B. and Peters, A. H. (2013) Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa. Nat. Struct. Mol. Biol., 20, 868-875.
5. Tang, F., Barbacioru, C., Wang, Y., Nordman, E., Lee, C., Xu, N., Wang, X., Bodeau, J., Tuch, B. B., Siddiqui, A. et al. (2009) mRNA-Seq whole-transcriptome analysis of a single cell. Nat. Methods, 6, 377-382.
6. Park, S. J., Komata, M., Inoue, F., Yamada, K., Nakai, K., Ohsugi, M. and Shirahige, K. (2013) Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. Genes Dev., 27, 2736-2748.
7. Shinagawa, T., Takagi, T., Tsukamoto, D., Tomaru, C., Huynh, L. M., Sivaraman, P., Kumarevel, T., Inoue, K., Nakato, R., Katou, Y. et al. (2014) Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells. Cell Stem Cell, 14, 217-227.
8. Carter, A. C., Davis-Dusenbery, B. N., Koszka, K., Ichida, J. K. and Eggan, K. (2014) Nanog-independent reprogramming to iPSCs with canonical factors. Stem Cell Rep., 2, 119-126.
9. Hamatani, T., Carter, M. G., Sharov, A. A. and Ko, M. S. (2004) Dynamics of global gene expression changes during mouse preimplantation development. Dev. Cell, 6, 117-131.
10. Zeng, F., Baldwin, D. A. and Schultz, R. M. (2004) Transcript profiling during preimplantation mouse development. Dev. Biol., 272, 483-496.
11. Pfeiffer, M. J., Siatkowski, M., Paudel, Y., Balbach, S. T., Baeumer, N., Crosetto, N., Drexler, H. C., Fuellen, G. and Boiani, M. (2011) Proteomic analysis of mouse oocytes reveals 28 candidate factors of the 'reprogrammome'. J. Proteome Res., 10, 2140-2153.
12. Macfarlan, T. S., Gifford, W. D., Driscoll, S., Lettieri, K., Rowe, H. M., Bonanomi, D., Firth, A., Singer, O., Trono, D., Pfaff, S. L. et al. (2012) Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature, 487, 57-63.
13. Wang, S., Kou, Z., Jing, Z., Zhang, Y., Guo, X., Dong, M., Wilmut, I. and Gao, S. (2010) Proteome of mouse oocytes at different developmental stages. Proc. Natl Acad. Sci., 107, 17639-17644.
14. Trapnell, C., Roberts, A., Goff, L., Pertea, G., Kim, D., Kelley, D. R., Pimentel, H., Salzberg, S. L., Rinn, J. L., Pachter, L. et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc., 7, 562-578.