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Series GSE40576 Query DataSets for GSE40576
Status Public on Feb 02, 2015
Title DNA Methylation Changes and Childhood Asthma in the Inner City [methylation]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Background: Epigenetic marks, like asthma, are heritable. They are influenced by the environment, direct the maturation of T cellslymphocytes, and have been shown to enhance the development of allergic airways disease in mice. Thus, we hypothesized that epigenetic marks are associated with allergic asthma in inner-city children. Methods: We compared methylation patterns and gene expression in inner-city children with persistent atopic asthma versus healthy controls, using DNA and RNA from peripheral blood mononuclear cells (PBMCs) from inner city children aged 6-12 years with persistent atopic asthma children and healthy controls. Results were externally validated with the GABRIELA study population. Results: Comparing asthmatics (N=97) to controls (N=97), we identified 81 regions that were differentially methylated. Several immune genes were hypomethylated in asthmatics, including IL-13, RUNX3, and a number of specific genes relevant to natural killer cells (KIR2DL4, KIR2DL3, KIR3DL1, and KLRD1) and T cells lymphocytes (TIGIT). 14 differentially methylated regions (DMRs) were associated with the serum IgE concentration of IgE, including RUNX3. These results were internally and externally validated with a global methylation assessment using a different methodology in our inner-city cohort and an independent European cohort (GABRIELA). Hypo- and hypermethylated genes tended to be associated with increased and decreased gene expression, respectively (P<0.6x10-11 for asthma and ; P<0.01 for IgE). To further explore the relationship between methylation and gene expression, we created a matrix of genomic changes in methylation versus transcriptional changes (methyl eQTL) for asthma, and identified cis- and trans-regulated genes whose expression was related to asthma asthma-associated methylation marks.
Overall design peripheral blood mononuclear cells (PBMCs) from 97 atopic asthmatic and 97 nonatopic nonasthmatic children
Contributor(s) Yang IV, Pedersen BS, Liu A, Schwartz DA
Citation(s) 25769910
Submission date Sep 04, 2012
Last update date Mar 22, 2019
Contact name David Schwartz
Phone 303-724-1783
Organization name University of Colorado, Anschutz Medical Campus
Department Medicine
Street address Anschutz Medical Campus
City Aurora
State/province CO
ZIP/Postal code 80045
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (194)
GSM996969 15-08-042-0_Nonasthmatic
GSM996970 15-04-009-4_Asthmatic
GSM996971 15-05-027-7_Asthmatic
This SubSeries is part of SuperSeries:
GSE40736 DNA Methylation Changes and Childhood Asthma in the Inner City
BioProject PRJNA174784

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
GSE40576_RAW.tar 183.1 Mb (http)(custom) TAR
GSE40576_matrix-raw-values.txt.gz 478.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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