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First published online July 6, 2006
Stem Cells Vol. 24 No. 11 November 2006, pp. 2522 -2528
doi:10.1634/stemcells.2006-0005; www.StemCells.com
© 2006 AlphaMed Press

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EMBRYONIC STEM CELLS: CHARACTERIZATION SERIES

More Than 40,000 Transcripts, Including Novel and Noncoding Transcripts, in Mouse Embryonic Stem Cells

Ryoko Araki, Ryutaro Fukumura, Naokazu Sasaki, Yasuji Kasama, Nobuko Suzuki, Hirokazu Takahashi, Yoshimichi Tabata, Toshiyuki Saito, Masumi Abe

Transcriptome Research Center, National Institute of Radiological Sciences, Chiba, Japan

Key Words. Embryonic stem cell • Mouse • Gene expression profiling • Low-abundance transcripts

Correspondence: Masumi Abe, Ph.D., Transcriptome Research Center National Institute of Radiological Sciences, Anagawa 4-9-1, Inage-ku, Chiba-shi, Chiba 263-8555, Japan. Telephone: 81-43-206-3219; Fax: 81-43-251-4593; e-mail: abemasum{at}nirs.go.jp

Received January 4, 2006; accepted for publication June 15, 2006.
First published online in STEM CELLS EXPRESS   July 6, 2006.



To study the transcriptome of embryonic stem cells, we used a new gene expression profiling method that can measure the expression levels of unknown and rarely expressed transcripts precisely. We detected a total of 33,136 signal peaks representing transcripts in mouse embryonic stem cells, E14. Subsequent random cloning of the peaks suggests that mouse embryonic stem cells express at least 40,000 transcripts, of which about 2,000 are still unknown. In addition, we identified 1,022 noncoding transcripts, several of which change depending on differentiation in gene expression. Our database provides a high-resolution expression profile of E14 cells and is applicable to other mouse embryonic stem cell analyses. It includes most transcription regulation factor-encoding genes and a significant number of unknown and noncoding transcripts.






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