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Mol. Hum. Reprod. Advance Access originally published online on September 5, 2007
Molecular Human Reproduction 2007 13(10):713-720; doi:10.1093/molehr/gam050
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© The Author 2007. Published by Oxford University Press on behalf of the European Society of Human Reproduction and Embryology. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Building comparative gene expression databases for the mouse preimplantation embryo using a pipeline approach to UniGene

J.-A.L. Stanton1,3, A.B. Macgregor2, C. Mason1, M. Dameh1 and D.P.L. Green1

1Anatomy and Structural Biology, University of Otago, 270 Great King Street, Dunedin 9001, New Zealand 2Centre for Comparative Genomics, Murdoch University, Murdoch 6150, Western Australia, Australia

3 Correspondence address. Tel: +64-3-479-7483; Fax: +64-3-479-7254; E-mail: jo.stanton{at}anatomy.otago.ac.nz

To understand early mammalian development there is a need to compare profiles of gene expression from different stages of the preimplantation mouse embryo. We describe here a method that uses gene expression data held in the UniGene database of the National Institutes of Health (NIH). The full mouse UniGene database (build #151) contains 43 104 gene clusters generated from ~4.1 million sequences. The Expressed Sequence Tags (EST) used to build UniGene are derived from cDNA libraries that are archived separately in the database of Expressed Sequence Tags (dbEST) database, with their own catalogue numbers. The mouse dbEST database contains 32 non-normalized dbEST libraries constructed from preimplantation stages (unfertilized oocyte, fertilized oocyte, 2-, 4-, 8- and 16-cell embryo and blastocyst). These libraries contain 219 852 EST sequences mapping to 15 731 UniGene clusters. We have developed a computational pipeline approach that imports and aggregates inventories of gene expression contained in these dbEST libraries. It uses these data to build an annotated web-based database of preimplantation gene expression with an in-built capacity for comparison of expression profiles. Comparison of gene expression profiles obtained for each developmental stage show statistically significant changes in gene expression during preimplantation development. These in silico-generated profiles were validated using RT–PCR.

Key words: database/EST/expression profiling/global gene expression/UniGene

Submitted on May 9, 2007; resubmitted on June 28, 2007; accepted on July 10, 2007.


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