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Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape

Kenneth Day1, Lindsay L Waite1, Anna Thalacker-Mercer24, Andrew West35, Marcas M Bamman245, James D Brooks6, Richard M Myers1 and Devin Absher1*

Author Affiliations

1 HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA

2 Departments Cell, Developmental, and Integrative Biology, the University of Alabama at Birmingham, Birmingham, AL 35294, USA

3 Department of Neurology, the University of Alabama at Birmingham, Birmingham, AL 35294, USA

4 The Center for Exercise Medicine, Birmingham, AL 35294, USA

5 The School of Medicine, Birmingham, AL 35294, USA

6 Stanford School of Medicine, Cancer Institute, Stanford, CA 94305, USA

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Genome Biology 2013, 14:R102  doi:10.1186/gb-2013-14-9-r102

Published: 13 September 2013

Additional files

Additional file 1:

Description of samples used in this study.

Format: DOCX Size: 58KB Download file

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Additional file 2:

Linear regression model results for ageCGs identified in each tissue separately.

Format: XLS Size: 1.2MB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 3:

UCSC Genome browser track for blood ageCGs.

Format: BED Size: 58KB Download file

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Additional file 4:

UCSC Genome browser track for brain ageCGs.

Format: BED Size: 74KB Download file

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Additional file 5:

UCSC Genome browser track for kidney ageCGs.

Format: BED Size: 167KB Download file

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Additional file 6:

UCSC Genome browser track for muscle ageCGs.

Format: BED Size: 61KB Download file

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Additional file 7:

Supplemental Figures S1 to S24.

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Additional file 8:

Multiple ageCGs affiliated with the same genes in blood.

Format: XLSX Size: 79KB Download file

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Additional file 9:

Multiple ageCGs affiliated with the same genes in brain.

Format: XLSX Size: 89KB Download file

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Additional file 10:

Multiple ageCGs affiliated with the same genes in kidney.

Format: XLSX Size: 146KB Download file

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Additional file 11:

Multiple ageCGs affiliated with the same genes in muscle.

Format: XLSX Size: 74KB Download file

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Additional file 12:

Top 5 unique and shared GO terms across tissues.

Format: XLSX Size: 71KB Download file

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Additional file 13:

Unique GO terms across tissues for positive ageCGs/genes.

Format: XLSX Size: 94KB Download file

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Additional file 14:

Unique GO terms across tissues for negative ageCGs/genes.

Format: XLSX Size: 61KB Download file

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Additional file 15:

Shared GO terms between at least two tissues for positive ageCGs/genes.

Format: XLSX Size: 97KB Download file

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Additional file 16:

Shared GO terms between at least three tissues for positive ageCGs/genes.

Format: XLSX Size: 67KB Download file

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Additional file 17:

Shared GO terms between all four tissues for positive ageCGs/genes.

Format: XLSX Size: 90KB Download file

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Additional file 18:

Shared GO terms between at least two tissues for negative ageCGs/genes.

Format: XLSX Size: 60KB Download file

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Additional file 19:

Unique and shared ageCGs/genes across all tissues.

Format: XLSX Size: 58KB Download file

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Additional file 20:

Blood unique ageCGs/genes only expressed within blood.

Format: XLSX Size: 64KB Download file

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Additional file 21:

Brain unique ageCGs/genes only expressed within brain.

Format: XLSX Size: 63KB Download file

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Additional file 22:

Kidney unique ageCGs/genes only expressed within kidney.

Format: XLSX Size: 98KB Download file

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Additional file 23:

Muscle unique ageCGs/genes only expressed within muscle.

Format: XLSX Size: 95KB Download file

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Additional file 24:

Target regions and primer sets used to synthesize probes for capture bisulfite sequencing to validate ageCGs identified by Methylation27 arrays, and linear mixed model results for each target containing coefficients, P-values, and q-values. Also included are Methylation27 CpGs that were covered by Bis-seq, associated IlluminaIDs, and q-values resulting from linear regression with age across all CpGs, and indication as to whether these same CpGs were significantly associated with age with linear regression results only across the same 19 samples that were bisulfite sequenced.

Format: XLSX Size: 27KB Download file

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