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Series GSE35069 Query DataSets for GSE35069
Status Public on Aug 03, 2012
Title Differential DNA Methylation in Purified Human Blood Cells
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Methylation of cytosines at CpG sites is a common epigenetic DNA modification that can be measured by a large number of methods, now even in a genome-wide manner for hundreds of thousands of sites. The application of DNA methylation analysis is becoming widely popular in complex disorders, for example, to understand part of the “missing inheritance”. The DNA samples most readily available for methylation studies are derived from whole blood. However, blood consists of many functionally and developmentally distinct cell populations in varying proportions. We studied whether such variation might affect the interpretation of methylation studies based on whole blood DNA. We found in healthy male blood donors there is important variation in the methylation profiles of whole blood, mononuclear cells, granulocytes, and cells from seven selected purified lineages. CpG methylation between mononuclear cells and granulocytes differed for 22% of the 8252 probes covering the selected 343 genes implicated in immune-related disorders by genome-wide association studies, and at least one probe was differentially methylated for 85% of the genes, indicating that whole blood methylation results might be unintelligible. For individual genes, even if the overall methylation patterns might appear similar, a few CpG sites in the regulatory regions may have opposite methylation patterns (i.e., hypo/hyper) in the main blood cell types. We conclude that interpretation of whole blood methylation profiles should be performed with great caution and for any differences implicated in a disorder, the differences resulting from varying proportions of white blood cell types should be considered.
Overall design Six healthy male blood donors, age 38 ± 13.6 years, were included in the study. From each individual, global DNA methylation levels were analyzed in whole blood, peripheral blood mononuclear cells (PBMC) and granulocytes as well as for seven isolated cell populations (CD4+ T cells, CD8+ T cells, CD56+ NK cells, CD19+ B cells, CD14+ monocytes, neutrophils, and eosinophils), n=60 samples analyzed in total.
Contributor(s) Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlén S, Greco D, Söderhäll C, Scheynius A, Kere J
Citation(s) 22848472, 30571772
Submission date Jan 12, 2012
Last update date Mar 22, 2019
Contact name Lovisa E Reinius
Organization name Karolinska Institutet
Department Department of Biosciences and Nutrition
Street address Novum, Halsovagen 7-9
City Huddinge
ZIP/Postal code 14157
Country Sweden
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (60)
GSM861635 WB_1
GSM861636 WB_2
GSM861637 WB_3
BioProject PRJNA150827

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
GSE35069_Matrix_signal_intensities.txt.gz 245.5 Mb (ftp)(http) TXT
GSE35069_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table

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