Transcriptome analysis of mouse stem cells and early embryos

Alexei A. Sharov, Yulan Piao, Ryo Matoba, Dawood B. Dudekula, Yong Qian, Vincent VanBuren, Geppino Falco, Patrick R. Martin, Carole A. Stagg, Uwem C. Bassey, Yuxia Wang, Mark G. Carter, Toshio Hamatani, Kazuhiro Aiba, Hidenori Akutsu, Lioudmila Sharova, Tetsuya S. Tanaka, Wendy L. Kimber, Toshiyuki Yoshikawa, Saied A. JaradatSerafino Pantano, Ramaiah Nagaraja, Kenneth R. Boheler, Dennis Taub, Richard J. Hodes, Dan L. Longo, David Schlessinger, Jonathan Keller, Emily Klotz, Garnett Kelsoe, Akihiro Umezawa, Angelo L. Vescovi, Janet Rossant, Tilo Kunath, Brigid L.M. Hogan, Anna Curci, Michele D’Urso, Janet Kelso, Winston Hide, Minoru S.H. Ko

Research output: Chapter in Book/Report/Conference proceedingChapter


Understanding and harnessing cellular potency are fundamental in biology and are also critical to the future therapeutic use of stem cells. Transcriptome analysis of these pluripotent cells is a first step towards such goals. Starting with sources that include oocytes, blastocysts, and embryonic and adult stem cells, we obtained 249,200 high-quality EST sequences and clustered them with public sequences to produce an index of approximately 30,000 total mouse genes that includes 977 previously unidentified genes. Analysis of gene expression levels by EST frequency identifies genes that characterize preimplantation embryos, embryonic stem cells, and adult stem cells, thus providing potential markers as well as clues to the functional features of these cells. Principal component analysis identified a set of 88 genes whose average expression levels decrease from oocytes to blastocysts, stem cells, postimplantation embryos, and finally to newborn tissues. This can be a first step towards a possible definition of a molecular scale of cellular potency. The sequences and cDNA clones recovered in this work provide a comprehensive resource for genes functioning in early mouse embryos and stem cells. The nonrestricted community access to the resource can accelerate a wide range of research, particularly in reproductive and regenerative medicine.

Original languageEnglish
Title of host publicationCurrent Research in Embryology
PublisherApple Academic Press
Number of pages21
ISBN (Electronic)9781466559905
ISBN (Print)9781926692814
Publication statusPublished - 01-01-2011
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • General Biochemistry,Genetics and Molecular Biology


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