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Series GSE66247 Query DataSets for GSE66247
Status Public on Feb 01, 2016
Title Methylation profiling of molar tissues caused by recessive maternal-effect NLRP7 mutations
Organism Homo sapiens
Experiment type Methylation profiling by genome tiling array
Summary Approximately 70% of women suffering with familial recurrent moles (RHM) are associated with recessive mutations of NLRP7, which cause the RHM by maternal-effect. It has been proposed that the phenotypes of molar pregnancies are associated with aberrant genomic imprinting. Using the Illumina Infinium HumanMethylation450 Beadchip arrays we characterize the genome-wide methylation profile of 4 molar samples and blood from the female patients. We confirm widespread loss-of-imprinting in the RHM samples but not in the blood-derived DNA from the asymptomatic female patients. The aberrant methylation at imprinted loci was confirmed using bisulphite PCR and subcloning or pyrosequencing. Finally, by comparing the methylation patterns observed in the RHM with normal placenta biopsies we identify many candidate maternally methylated regions, consistent with novel imprinted genes.
Overall design DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel. Bisulfite conversion of 600 ng of each sample was perform according to the manufacturer's recommendation for Illumina Infinium Assay. Effective bisulphite conversion was checked for three controls that were converted simultaneously with the samples. 4 ul of bisulfite converted DNA were used to hybridize on Infinium HumanMethylation 450 BeadChip, following Illumina Infinium HD Methylation protocol. Chip analysis was performed using Illumina HiScan SQ fluorescent scanner. The intensities of the images are extracted using GenomeStudio (2011.2) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.
Contributor(s) Monk D, Fisher R
Citation(s) 26544189
Submission date Feb 24, 2015
Last update date Mar 22, 2019
Contact name David Monk
Organization name IDIBELL
Department PEBC
Street address 199-203 Av. Gran Via de L' Hospitalet
City LĀ“Hospitalet de Llobregat
State/province Barcelona
ZIP/Postal code 80908
Country Spain
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (8)
GSM1617941 Blood_1
GSM1617942 Blood_2
GSM1617943 Blood_3
BioProject PRJNA276263

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
GSE66247_RAW.tar 183.1 Mb (http)(custom) TAR
GSE66247_signals.txt.gz 35.0 Mb (ftp)(http) TXT
Processed data included within Sample table

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