GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE62219 Query DataSets for GSE62219
Status Public on Apr 01, 2015
Title Age-associated DNA methylation changes within 5 years after birth in human blood leukocytes
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Age-related changes in DNA methylation occurring in blood leukocytes during early childhood may reflect epigenetic maturation. We hypothesized that some of these changes involve gene networks of critical relevance in leukocyte biology and conducted a prospective study to elucidate the dynamics of DNA methylation. Serial blood samples were collected at 3, 6, 12, 24, 36, 48 and 60 months after birth in 10 healthy girls born in Finland and participating in the Type 1 Diabetes Prediction and Prevention Study. DNA methylation was measured using the HumanMethylation450 BeadChip. After filtering for the presence of polymorphisms and cell-lineage-specific signatures, 794 CpGs showed significant DNA methylation differences as a function of age in all children (41.5% age-methylated and 58.4% age-demethylated, bonferroni corrected p-value <0.001). Age-methylated CpGs were more frequently located in gene bodies and within +5 to +50 kilobases (kb) of transcription start sites (TSS), and enriched in developmental, neuronal and plasma membrane genes. Age-demethylated CpGs were associated to promoters and DNAse-I hypersensitivity sites, located within -5 to +5 kb of the nearest TSS, and enriched in genes related to immunity, antigen presentation, the polycomb-group protein complex and cytoplasm. This study reveals that susceptibility loci for complex inflammatory diseases (e.g. IRF5, NOD2, PTGER4) and genes encoding histone modifiers and chromatin remodeling factors (e.g. HDAC4, KDM2A, KDM2B, JARID2, ARID3A, SMARCD3) undergo DNA methylation changes in leukocytes during early childhood. These results open new perspectives to understand leukocyte maturation and provide a catalog of CpGs that may need to be corrected for age effects when performing DNA methylation studies in children.
Overall design We analysed the longitudinal changes in DNA methylation in a total of 60 samples at 3, 6, 12, 24, 36, 48, and 60 months after birth, using serial DNA samples extracted from peripheral blood leukocytes of 10 healthy girls of the Diabetes Prediction and Prevention Study (DIPP).
Contributor(s) Acevedo N, Reinius LE, Vitezic M, Fortino V, Söderhäll C, Honkanen H, Veijola R, Simell O, Toppari J, Ilonen J, Knip M, Scheynius A, Hyöty H, Greco D, Kere J
Citation(s) 25874017
Submission date Oct 09, 2014
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)
GSM1522958 Girl1_month3
GSM1522959 Girl1_month12
GSM1522960 Girl1_month24
BioProject PRJNA263492

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
GSE62219_RAW.tar 667.5 Mb (http)(custom) TAR (of IDAT)
GSE62219_processed_DIPP.txt.gz 128.7 Mb (ftp)(http) TXT
GSE62219_signal_intenstities_DIPP.txt.gz 135.9 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap