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Series GSE115508 Query DataSets for GSE115508
Status Public on Nov 06, 2018
Title DNA methylation profiling of acute chorioamnionitis-associated placentas and fetal membranes : insights into epigenetic variation in spontaneous preterm births
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Acute chorioamnionitis (aCA) is a commonly reported histologic lesion in at least 40% of spontaneous preterm deliveries. It is typically characterized by an infiltration of maternal neutrophils into the chorioamniotic membranes and is also associated with other placental inflammatory lesions such as acute intervillositis and acute villitis. DNA methylation (DNam) is an easily measurable epigenetic mark, which is more stable than mRNA. While DNAm may influence gene expression in specific cell types, it may also reflect altered cell composition. Studies have previously documented aCA-associated cellular changes primarily in the context of a polymicrobial invasion of the amniotic space. We, thus hypothesize that changes in DNAm associated with aCA will occur predominantly as a consequence of the response to infection, in particular due to alterations in the number of neutrophils and/or other alterations in cell populations inherent to the placenta. Pooled chorionic villus samples (22 aCA cases, 22 non-aCA cases) and fetal membranes (amnion and chorion) (9 aCA cases, 7 non-aCA cases) were evaluated using the Illumina EPIC array, which quantifies DNAm at >850,000 sites in the genome. We identified 66 differentially methylated sites associated with aCA (FDR <0.15, methylation difference >0.05). At the same thresholds, ~20% chorionic villi sites were also differentially methylated in chorion, but none were observed in amnion. Using publicly available datasets, we identified 2069 neutrophil-specific CpGs by differential methylation analysis. Euclidean clustering of our chorionic villi DNAm data (n=44 samples) using 2069 neutrophil-specific CpG sites largely separated aCA cases from the non-aCA cases, suggesting activation of innate immune responses in aCA-associated placentas.
 
Overall design Placental samples from 44 preterm placentas (chorionic villi), and matched chorion and amnion for 16 of these cases were were profiled using theInfinium HumanMethylation850 BeadChip. 4 chorionic villi samples were run in duplicates as technical replicates
 
Contributor(s) Konwar C, Robinson WP
Citation(s) 30373633
Submission date Jun 08, 2018
Last update date Jan 20, 2019
Contact name Wendy Robinson
E-mail(s) wprobinsonlab@gmail.com
Organization name University of British Columbia
Department Medical Genetics
Lab Robinosn
Street address 950 W 28th Ave
City Vancouver
State/province BC
ZIP/Postal code V5Z 4H4
Country Canada
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (79)
GSM3179712 PL78_vc
GSM3179713 PL23_vc
GSM3179714 PL29_vc
Relations
BioProject PRJNA475230

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
GSE115508_RAW.tar 1.2 Gb (http)(custom) TAR (of IDAT)
GSE115508_aCA_averagebetas_processed_amnion.csv.gz 85.5 Mb (ftp)(http) CSV
GSE115508_aCA_averagebetas_processed_chorion.csv.gz 91.4 Mb (ftp)(http) CSV
GSE115508_aCA_averagebetas_processed_villi.csv.gz 269.1 Mb (ftp)(http) CSV
GSE115508_aCA_signal_intensities_raw.csv.gz 614.4 Mb (ftp)(http) CSV
Processed data are available on Series record

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