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. 2009 Jan 15:2:3.
doi: 10.1186/1755-8794-2-3.

Detailed transcriptome atlas of the pancreatic beta cell

Burak Kutlu  1 , David Burdick, David Baxter, Joanne Rasschaert, Daisy Flamez, Decio L Eizirik, Nils Welsh, Nathan Goodman, Leroy Hood
Affiliations

Detailed transcriptome atlas of the pancreatic beta cell

Burak Kutlu et al. BMC Med Genomics. .

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).

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Figures

Figure 1
Figure 1
A) Histogram of the signature counts in the raw MPSS dataset (before annotation). The frequencies of signature logarithm 2 scale counts in both MPSS samples are plotted. B) Scatter plot of signature counts first islet sample (on x axis) vs second islet sample (on y axis). Tpm = transcripts per million.
Figure 2
Figure 2
'β Cell Gene Atlas' results page. If a gene is estimated to be present at a high level, it is denoted with a darker cell color. The intermediate abundances are indicated with lighter cell colors. Genes expressed with a probability score of 0.95 or higher are designated with a red border color. The results can be viewed either with by "species" or "tissue" groupings. The actual values used to draw the heatmap or the probability scores can be viewed with "gene rank" or "probability" view, respectively.
Figure 3
Figure 3
Hierarchical clustering of tissue expression profiles: The two main branches of the group are β cells/cell lines and islets/pancreas. h_beta: Human beta cells, m_min6: MIN6 cells, r_beta: rat beta cells, r_INS: INS-1 cells, r_panc: Rat pancreas, r_alpha: Rat alpha cells, r_isl: Rat islets, m_isl: Mouse islets, m_panc: mouse pancreas, h_duct: human ductal cells, h_isl: Human islets, h_exoc: Human exocrine cells.
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