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Series GSE62924 Query DataSets for GSE62924
Status Public on Nov 03, 2014
Title Prenatal arsenic exposure and the epigenome: Identifying sites of 5-methyl cytosine alterations that predict functional changes in gene expression in newborn cord blood and subsequent birth outcomes
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Prenatal exposure to inorganic arsenic (iAs) is detrimental to the health of newborns and increases the risk of disease development later in life. Here we examined a subset of newborn cord blood leukocyte samples collected from mothers enrolled in the Biomarkers of Exposure to ARsenic (BEAR) pregnancy cohort in Gomez Palacio, Mexico who were exposed to a range of drinking water arsenic concentrations (0.456-236 µg/L). Changes in iAs-associated DNA 5-methyl cytosine methylation were assessed across 424,935 CpG sites representing 18,761 genes and were compared to corresponding expression levels and birth outcomes. In the context of arsenic exposure, a total of 2,705 genes were identified with iAs-associated differences in DNA methylation. Site-specific analyzes identified DNA methylation changes that were most predictive of gene expression levels. Specifically, CpG methylation within CpG islands positioned within the first exon and 200bp upstream of the transcription start site yielded the most significant association with gene expression levels. A set of 16 genes was identified with correlated iAs-associated changes in DNA methylation and mRNA expression and all were highly enriched for binding sites of the early growth response (EGR) and CCCTC-binding factor (CTCF) transcription factors. Furthermore, DNA methylation levels of seven of these genes were associated with differences in birth outcomes including gestational age, placental weight and head circumference. These data highlight the complex interplay between DNA methylation and functional changes in gene expression and health outcomes and underscore the need for functional analyzes coupled to epigenetic assessments.
 
Overall design 48 DNA methylation profiles were obtained but only 38 samples corresponding to samples also analyzed for gene expression (see Rager 2014) were further normalized and used in the publication from the Biomarkers of Arsenic (BEAR) cohort were analyzed for DNA methylation profiles.
 
Contributor(s) Rojas D, Rager  JE, Smeester  L, Bailey  KA, Drobnà Z, Rubio-Andrade M, Styblo M, Garcia-Vargas G, Fry RC
Citation(s) 25304211
Submission date Nov 03, 2014
Last update date Mar 22, 2019
Contact name Jose Daniel Rojas Rojas
E-mail(s) rojasroj@email.unc.edu
Phone 6173090920
Organization name University of North Carolina at Chapel Hill
Department Environmental Science and Engineering
Lab Fry Lab
Street address MHRC 0032
City Old Pittsboro Rd.
State/province NC
ZIP/Postal code 27516
Country USA
 
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (38)
GSM1536317 Genomic DNA from cord blood leukocytes C128
GSM1536318 Genomic DNA from cord blood leukocytes C095
GSM1536319 Genomic DNA from cord blood leukocytes C221
Relations
BioProject PRJNA266110

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
GSE62924_RAW.tar 183.1 Mb (http)(custom) TAR
GSE62924_Readme_characteristics.xlsx 45.5 Kb (ftp)(http) XLSX
GSE62924_raw.csv.gz 161.7 Mb (ftp)(http) CSV
Processed data included within Sample table
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