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| Status |
Public on Oct 08, 2010 |
| Title |
Evaluation of affinity-based genome-wide DNA methylation data: effects of CpG density, amplification bias and copy number variation |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
Methylation profiling by high throughput sequencing
Genome variation profiling by SNP array
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| Summary |
Abstract: DNA methylation is an essential epigenetic modification that plays a key role associated with the regulation of gene expression during differentiation but in disease states such as cancer, the DNA methylation landscape is often deregulated. There are now numerous technologies available to interrogate DNA methylation status of CpG sites in a targeted or genome-wide fashion but each method, due to intrinsic biases, potentially interrogates different fractions of the genome. In this study, affinity-purification of methylated DNA using two popular genome-wide techniques: methylated DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain-based capture (MBDCap) were evaluated, highlighting that each technique operates in a different domain of the CpG density landscape. The effect of whole genome amplification was explored, illustrating that it can reduce sensitivity for detecting DNA methylation in GC-rich regions of the genome. Using MBDCap, microarray- and sequencing-based readouts were compared, highlighting the impact that copy number variation (CNV) can make in differential comparisons of methylomes. These studies reveal that the analysis of DNA methylation data and genome coverage is highly dependent on the method employed and consideration must be made in light of GC content, extent of DNA amplification and copy number.
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| Overall design |
Comparison of MeDIP/MBD for DNA methylation profiling, comparison of whole genome amplification techniques, using tiling array for copy number aberration detection and comparisons of tiling array data to sequencing readouts
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| Contributor(s) |
Robinson MD |
| Citation(s) |
21045081, 21788347 |
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| Submission date |
Oct 06, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark Robinson |
| E-mail(s) |
[email protected]
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| Organization name |
University of Zuerich
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| Department |
Institute of Molecular Life Sciences
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| Street address |
Winterthurerstrasse 190
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| City |
Zuerich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platforms (3) |
| GPL5082 |
[Hs_PromPR] Affymetrix Human Promoter 1.0R Array |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
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| Samples (40)
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| Relations |
| SRA |
SRP003788 |
| BioProject |
PRJNA132579 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE24546_MeDIP-chip_results.tar.gz |
1.5 Mb |
(ftp)(http) |
TAR |
| GSE24546_RAW.tar |
3.1 Gb |
(http)(custom) |
TAR (of CEL, MAP, TXT) |
| GSE24546_TSS_counts.txt.gz |
137.8 Kb |
(ftp)(http) |
TXT |
| GSE24546_blocksStats_diffMeth.txt.gz |
769.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data included within Sample table |
| Raw data are available in SRA |
| Processed data are available on Series record |
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