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Series GSE35204 Query DataSets for GSE35204
Status Public on Mar 08, 2012
Title Methylome-wide comparison of human genomic DNA extracted from whole blood and from EBV-transformed lymphocyte cell lines
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary DNA from Epstein-Barr virus (EBV)-transformed lymphocyte cell lines (LCLs) has proven very useful for studies of genetic sequence polymorphisms. Whether EBV-LCL DNA is suitable for methylation studies is less clear. We conduct a genome-wide methylation investigation using an array set with 45 million probes to investigate the methylome of EBV-LCL DNA and technical duplicates of whole blood (WB) DNA from the same 10 individuals. Methylation sites that show variation between individuals are potentially useful as biomarkers in disease studies. Our comparison is, therefore, focused specifically on these methylation variable sites. The sample correlations (i.e., a measure of whether the rank of the signals remains consistent between two samples from the same individual) for the methylation variable probes ranged from 0.69-0.78 for the WB duplicates and from 0.27-0.72 for WB versus EBV-LCL. To compare the pattern of the methylation signals, we grouped adjacent probes based on their inter-correlations. These analyses showed ~29,000 blocks in WB and ~14,000 blocks in EBV-LCL. Furthermore, merely 31% of the methylated regions detected in WB were detectable in EBV-LCLs. Our study shows that there are substantial differences in the DNA methylation patterns between EBV-LCL and WB. Thus, EBV-LCL DNA cannot be used as a proxy for WB DNA in methylation studies.
 
Overall design The methylation of technical duplicates of DNA extracted from whole blood from 10 individuals, as well as DNA extracted from EBV-transformed lymphocyte cell lines (EBV-LCL) from the same samples of whole blood, are investigated using the Affymetrix GeneChip Human Tiling 2.0R array set. In total, 30 samples from 10 individuals were investigated on 7 arrays.

The supplementary "GSE35204_ChrXX_bgc_qt.txt" files contain the background-corrected and quantile-normalized data for all 30 samples per chromosome. The files include 32 columns: 'Seq' refers to the chromosome, 'Pos' indicates the position in the genome on that chromosome, and columns 3-32 indicate the sample numbers.
 
Contributor(s) Aberg K, Khachane AN, Rudolf G, Nerella S, Fugman DA, Tischfield JA, van den Oord EJ
Citation(s) 22378283
Submission date Jan 18, 2012
Last update date Mar 21, 2017
Contact name Karolina A Aberg
Organization name Virginia Commonwealth University
Department Center for Biomarker Resarch & Personalized Medicine
Street address 1112 East Clay Street
City Richmond
State/province VA
ZIP/Postal code 23298
Country USA
 
Platforms (7)
GPL4910 [Hs35b_P01R] Affymetrix Human Tiling 2.0R Set, Array 1
GPL4911 [Hs35b_P02R] Affymetrix Human Tiling 2.0R Set, Array 2
GPL4912 [Hs35b_P03R] Affymetrix Human Tiling 2.0R Set, Array 3
Samples (210)
GSM863479 Whole blood, individual 1, rep 1, array 1
GSM863480 Whole blood, individual 1, rep 2, array 1
GSM863481 EBV-LCL, individual 1, array 1
Relations
BioProject PRJNA150693

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
GSE35204_Chr01_bgc_qt.txt.gz 457.0 Mb (ftp)(http) TXT
GSE35204_Chr02_bgc_qt.txt.gz 496.0 Mb (ftp)(http) TXT
GSE35204_Chr03_bgc_qt.txt.gz 391.0 Mb (ftp)(http) TXT
GSE35204_Chr04_bgc_qt.txt.gz 352.1 Mb (ftp)(http) TXT
GSE35204_Chr05_bgc_qt.txt.gz 350.6 Mb (ftp)(http) TXT
GSE35204_Chr06_bgc_qt.txt.gz 344.4 Mb (ftp)(http) TXT
GSE35204_Chr07_bgc_qt.txt.gz 303.7 Mb (ftp)(http) TXT
GSE35204_Chr08_bgc_qt.txt.gz 280.9 Mb (ftp)(http) TXT
GSE35204_Chr09_bgc_qt.txt.gz 240.5 Mb (ftp)(http) TXT
GSE35204_Chr10_bgc_qt.txt.gz 267.0 Mb (ftp)(http) TXT
GSE35204_Chr11_bgc_qt.txt.gz 261.8 Mb (ftp)(http) TXT
GSE35204_Chr12_bgc_qt.txt.gz 252.1 Mb (ftp)(http) TXT
GSE35204_Chr13_bgc_qt.txt.gz 192.6 Mb (ftp)(http) TXT
GSE35204_Chr14_bgc_qt.txt.gz 173.5 Mb (ftp)(http) TXT
GSE35204_Chr15_bgc_qt.txt.gz 164.9 Mb (ftp)(http) TXT
GSE35204_Chr16_bgc_qt.txt.gz 157.3 Mb (ftp)(http) TXT
GSE35204_Chr17_bgc_qt.txt.gz 160.7 Mb (ftp)(http) TXT
GSE35204_Chr18_bgc_qt.txt.gz 154.4 Mb (ftp)(http) TXT
GSE35204_Chr19_bgc_qt.txt.gz 95.0 Mb (ftp)(http) TXT
GSE35204_Chr20_bgc_qt.txt.gz 121.7 Mb (ftp)(http) TXT
GSE35204_Chr21_bgc_qt.txt.gz 70.1 Mb (ftp)(http) TXT
GSE35204_Chr22_bgc_qt.txt.gz 72.4 Mb (ftp)(http) TXT
GSE35204_RAW.tar 5.1 Gb (http)(custom) TAR (of CEL)
Processed data are available on Series record
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