Open Access Research article

Functional annotations of diabetes nephropathy susceptibility loci through analysis of genome-wide renal gene expression in rat models of diabetes mellitus

Yaomin Hu1, Pamela J Kaisaki1, Karène Argoud1, Steven P Wilder1, Karin J Wallace1, Peng Y Woon1, Christine Blancher1, Lise Tarnow2, Per-Henrik Groop3, Samy Hadjadj4, Michel Marre5, Hans-Henrik Parving6, Martin Farrall1, Roger D Cox7, Mark Lathrop8, Nathalie Vionnet9, Marie-Thérèse Bihoreau1 and Dominique Gauguier110*

Author Affiliations

1 The Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK

2 Steno Diabetes Center, Copenhagen, Denmark

3 Department of Medicine, Division of Nephrology, Helsinki University Central Hospital and Folkhälsan Institute of Genetics, Helsinki, Finland

4 CHU Poitiers, University Hospital, Endocrinology and INSERM, ERM 324, Poitiers, France

5 Department of Diabetology, Bichat Hospital and INSERM, U695, Xavier Bichat University of Medicine, Paris, France

6 Department of Medical Endocrinology, Rigshospitalet, University Hospital of Copenhagen, Copenhagen, Denmark

7 MRC Mammalian Genome Unit, Harwell OX11 0RD, UK

8 National Genotyping Centre, Evry, France

9 INSERM, UMR S 525, Université Pierre et Marie Curie-Paris 6, Paris, France

10 INSERM, U872, Centre de Recherche des Cordeliers, Paris, France

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BMC Medical Genomics 2009, 2:41  doi:10.1186/1755-8794-2-41

Published: 9 July 2009

Additional files

Additional file 1:

Oligonucleotides designed for QRT-PCR analysis of renal gene transcription regulation in diabetic and control rats. Details of symbols, descriptions and GenBank accession numbers of genes tested for differential expression between GK, STZ-WKY and WKY rats using QRT-PCR, alongwith primer sequence and PCR product length.

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Additional file 2:

Phenotypic features of GK, STZ-WKY and WKY rats. Body weight and plasma glucose concentrations in GK, STZ-WKY and WKY rats.

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Additional file 3:

Photomicrographs of PAS-stained kidney sections from GK, STZ-WKY and WKY rats (×400). Renal histopathological features in the diabetic strains (GK, STZ-WKY) and in WKY normoglycaemic controls.

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Additional file 4:

Details of genes differentially expressed in kidneys of GK and STZ-WKY models of diabetes and WKY controls. Details of Affymetrix probeset references, symbols and descriptions of genes found significantly differentially expressed (P < 0.05) between diabetic rats (GK, STZ-WKY) and WKY controls, alongwith calculation of transcription fold change and statistical significance of transcriptional changes.

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Additional file 5:

Overview of renal transcriptomic changes in pathways underlying differential gene expression adaptations to moderate or severe hyperglycaemia in rat models of diabetes. Selection of the most significant functionally related groups of genes found differentially expressed between diabetic rats (GK, STZ-WKY) and WKY controls.

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Additional file 6:

Comparison of Affymetrix and Illumina kidney gene expression profiling data for genes found differentially expressed between GK, STZ-WKY and WKY rats using the Affymetrix platform. Replication analysis of Affymetrix-based gene expression changes between GK, STZ-WKY and WKY rats using data from Illumina arrays showing fold-changes and statistical significance of differential expression derived by the two microarray technologies.

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Additional file 7:

Genes mapped to chromosomal regions of the rat genome conserved with human DN loci and found not differentially expressed between diabetic models. Details of Affymetrix probeset references, symbols and descriptions of rat genes localised in genomic regions homologous to human DN susceptibility loci, and not significantly differentially expressed (P > 0.05) between diabetic rats (GK, STZ-WKY) and WKY controls, alongwith calculation of transcription fold change and statistical significance of transcriptional changes.

Format: XLS Size: 72KB Download file

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