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Series GSE24546 Query DataSets for GSE24546
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
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.
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
Contributor(s) Robinson MD
Citation(s) 21045081, 21788347
Submission date Oct 06, 2010
Last update date May 15, 2019
Contact name Mark Robinson
Organization name University of Zuerich
Department Institute of Molecular Life Sciences
Street address Winterthurerstrasse 190
City Zuerich
ZIP/Postal code 8057
Country Switzerland
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)
Samples (40)
GSM605080 LNCaP MBDCap-SF (lane 1)
GSM605081 LNCaP MBDCap-SF (lane 2)
GSM605082 PrEC MBDCap-SF (lane 1)
SRA SRP003788
BioProject PRJNA132579

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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 SelectorHelp
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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