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Detailed transcriptome atlas of the pancreatic beta cell

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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).
Keywords
NATIONAL-CENTER, HIGH GLUCOSE, SYSTEMS BIOLOGY, DATABASE RESOURCES, BIOTECHNOLOGY-INFORMATION, SIGNATURE SEQUENCING MPSS, GENE-EXPRESSION, NETWORKS, ISLETS, IDENTIFICATION

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MLA
Kutlu, Burak et al. “Detailed Transcriptome Atlas of the Pancreatic Beta Cell.” BMC MEDICAL GENOMICS 2 (2009): n. pag. Print.
APA
Kutlu, Burak, Burdick, D., Baxter, D., Rasschaert, J., Flamez, D., Eizirik, D. L., Welsh, N., et al. (2009). Detailed transcriptome atlas of the pancreatic beta cell. BMC MEDICAL GENOMICS, 2.
Chicago author-date
Kutlu, Burak, David Burdick, David Baxter, Joanne Rasschaert, Daisy Flamez, Décio L Eizirik, Nils Welsh, Nathan Goodman, and Leroy Hood. 2009. “Detailed Transcriptome Atlas of the Pancreatic Beta Cell.” Bmc Medical Genomics 2.
Chicago author-date (all authors)
Kutlu, Burak, David Burdick, David Baxter, Joanne Rasschaert, Daisy Flamez, Décio L Eizirik, Nils Welsh, Nathan Goodman, and Leroy Hood. 2009. “Detailed Transcriptome Atlas of the Pancreatic Beta Cell.” Bmc Medical Genomics 2.
Vancouver
1.
Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, Eizirik DL, et al. Detailed transcriptome atlas of the pancreatic beta cell. BMC MEDICAL GENOMICS. 2009;2.
IEEE
[1]
B. Kutlu et al., “Detailed transcriptome atlas of the pancreatic beta cell,” BMC MEDICAL GENOMICS, vol. 2, 2009.
@article{847019,
  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).},
  author       = {Kutlu, Burak and Burdick, David and Baxter, David and Rasschaert, Joanne and Flamez, Daisy and Eizirik, Décio L and Welsh, Nils and Goodman, Nathan and Hood, Leroy},
  issn         = {1755-8794},
  journal      = {BMC MEDICAL GENOMICS},
  keywords     = {NATIONAL-CENTER,HIGH GLUCOSE,SYSTEMS BIOLOGY,DATABASE RESOURCES,BIOTECHNOLOGY-INFORMATION,SIGNATURE SEQUENCING MPSS,GENE-EXPRESSION,NETWORKS,ISLETS,IDENTIFICATION},
  language     = {eng},
  title        = {Detailed transcriptome atlas of the pancreatic beta cell},
  url          = {http://dx.doi.org/10.1186/1755-8794-2-3},
  volume       = {2},
  year         = {2009},
}

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