Research article

Detailed transcriptome atlas of the pancreatic beta cell

Burak Kutlu¹ , David Burdick¹ , David Baxter¹ , Joanne Rasschaert² , Daisy Flamez² , Decio L Eizirik² , Nils Welsh³ , Nathan Goodman¹ and Leroy Hood¹

¹Institute for Systems Biology, Seattle, WA, USA

²Laboratory of Experimental Medicine, Universite Libre de Bruxelles, Brussels, Belgium

³Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden

author email corresponding author email

BMC Medical Genomics 2009, 2:3doi:10.1186/1755-8794-2-3

Published:	15 January 2009

Abstract

Background

Gene expression patterns provide a detailed view of cellular functions. Comparison of profiles in disease vs normal conditions provides insights into the processes underlying disease progression. However, availability and integration of public gene expression datasets remains a major challenge. The aim of the present study was to explore the transcriptome of pancreatic islets and, based on this information, to prepare a comprehensive and open access inventory of insulin-producing beta cell gene expression, the Beta Cell Gene Atlas (BCGA).

Methods

We performed Massively Parallel Signature Sequencing (MPSS) analysis of human pancreatic islet samples and microarray analyses of purified rat beta cells, alpha cells and INS-1 cells, and compared the information with available array data in the literature.

Results

MPSS analysis detected around 7600 mRNA transcripts, of which around a third were of low abundance. We identified 2000 and 1400 transcripts that are enriched/depleted in beta cells compared to alpha cells and INS-1 cells, respectively. Microarray analysis identified around 200 transcription factors that are differentially expressed in either beta or alpha cells. We reanalyzed publicly available gene expression data and integrated these results with the new data from this study to build the BCGA. The BCGA contains basal (untreated conditions) gene expression level estimates in beta cells as well as in different cell types in human, rat and mouse pancreas. Hierarchical clustering of expression profile estimates classify cell types based on species while beta cells were clustered together.

Conclusion

Our gene atlas is a valuable source for detailed information on the gene expression distribution in beta cells and pancreatic islets along with insulin producing cell lines. The BCGA tool, as well as the data and code used to generate the Atlas are available at the T1Dbase website (T1DBase.org).