Open Access Highly Accessed Research article

Effects of palmitate on genome-wide mRNA expression and DNA methylation patterns in human pancreatic islets

Elin Hall1, Petr Volkov1, Tasnim Dayeh1, Karl Bacos1, Tina Rönn1, Marloes Dekker Nitert2 and Charlotte Ling1*

Author Affiliations

1 Epigenetics and Diabetes Unit, Department of Clinical Sciences, Lund University Diabetes Centre, CRC, Lund University, Scania University Hospital, Malmö, Sweden

2 School of Medicine, Royal Brisbane Clinical School, The University of Queensland, Herston, QLD 4006, Australia

For all author emails, please log on.

BMC Medicine 2014, 12:103  doi:10.1186/1741-7015-12-103

Published: 23 June 2014

Additional files

Additional file 1: Table S1:

Characteristics of the human pancreatic donors included in the DNA methylation array analysis.

Format: PDF Size: 7KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2: Table S2:

Differentially expressed genes in human islets exposed to palmitate compared with the control (q <0.05).

Format: XLS Size: 883KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 3: Table S3:

Biological pathways including all genes that exhibit differential mRNA expression (q <0.05) in human pancreatic islets exposed to palmitate compared to control treatment.

Format: PDF Size: 53KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 4: Table S4:

Biological pathways including genes that exhibit decreased mRNA expression (q <0.05) in human pancreatic islets exposed to palmitate compared to control treatmet.

Format: PDF Size: 50KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 5: Table S5:

Biological pathways including genes that exhibit increased mRNA expression (q <0.05) in human pancreatic islets exposed to palmitate compared to control treatmet.

Format: PDF Size: 13KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 6: Table S6:

Differential mRNA expression (q <0.05) of candidate genes for type 2 diabetes (T2D) in human pancreatic islets exposed to palmitate versus control. DNA methylation data are displayed if the absolute difference in DNA methylation ≥3% and P <0.05.

Format: PDF Size: 76KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 7: Table S7:

Differential mRNA expression (q <0.05) of candidate genes for type 2 diabetes (T2D) related traits in human pancreatic islets exposed to palmitate versus control. DNA methylation data are displayed if the absolute difference in DNA methylation ≥3% and P <0.05.

Format: PDF Size: 77KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 8: Table S8:

Differential mRNA expression (q <0.05) of candidate genes for obesity in human pancreatic islets exposed to palmitate versus control. DNA methylation data are displayed if the absolute difference in DNA methylation ≥3% and P <0.05.

Format: PDF Size: 77KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 9: Table S9:

Global DNA methylation in human pancreatic islets exposed to palmitate compared to control treatment. Average DNA methylation (%) in gene- and CpG-regions in human pancreatic islets treated for 48 h with control media or palmitate-containing media.

Format: PDF Size: 16KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 10: Table S10:

CpG sites with differential DNA methylation in human pancreatic islets exposed to palmitate compared to control treatment P <0.05.

Format: XLS Size: 7.9MB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data

Additional file 11: Table S11:

Differential mRNA expression (q <0.05) of genes with a corresponding change in DNA methylation (P <0.05 and absolute DNA methylation difference ≥3%) of the nearest gene, in human pancreatic islets exposed to palmitate versus control.

Format: PDF Size: 780KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 12: Figure S1:

Results from KEGG pathway analysis using genes that exhibit differential DNA methylation (P <0.05) in human pancreatic islets exposed to palmitate compared to control treatment. It includes only pathways which also displayed enrichment for genes with differential expression after palmitate treatment in human pancreatic islets.

Format: PDF Size: 221KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 13: Table S12:

Biological pathways including genes that exhibit differential DNA methylation (P <0.05) in human pancreatic islets exposed to palmitate compared to control teatment. It includes only pathways which also displayed enrichment for genes with differential expression after palmitate treatment in human pancreatic islets.

Format: PDF Size: 32KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 14: Table S13:

Infinium HumanMethylation450K BeadChip array probes with possible cross reactivity to other locations in the genome.

Format: PDF Size: 89KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 15: Table S14:

Genes displaying significant difference in mRNA expression between control and palmitate-treated human pancreatic islets (q <0.05) as well as significant correlation between BMI and mRNA expression in human pancreatic islets (P <0.05).

Format: PDF Size: 93KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 16: Table S15:

Differentially expressed genes (P <0.05) in islets from T2D versus non-diabetic donors overlapping with the 1,860 genes with altered expression in the palmitate-exposed islets.

Format: XLS Size: 38KB Download file

This file can be viewed with: Microsoft Excel Viewer

Open Data