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Series GSE46168 Query DataSets for GSE46168
Status Public on Apr 22, 2013
Title Inactive or moderately active human promoters are enriched for inter-individual epialleles [Methylation BeadChip]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary We first demonstrate that non-genetically determined inter-individual differentially methylated regions (iiDMRs) can be temporally stable for at least two years. Then, we show that iiDMRS are associated with concomitant changes in chromatin state as measured by inter-individual differences in the levels of the histone variant H2A.Z. However, the correlation of promoter iiDMRs with gene expression is negligible and this correlation is not improved even by integrating H2A.Z information. We find that most promoter epialleles, whether genetically or non-genetically determined, are associated with low levels of transcriptional activity, depleted for house keeping genes, and either depleted for H3K4me3/enriched for H3K27me3, or lacking both these marks in human embryonic stem cells. These findings validate in an independent cohort. Interestingly, the key features of iiDMRs are reminiscent of those previously observed for promoters that undergo hyper-methylation in various cancers, in vitro cell culture, and human chronological ageing.
Overall design DNA Methylation, H2A.z ChIP-seq, RNA-seq (submitted) separately were collected for five normal individuals (samples with "T" prefixes). T21/T22 and T31/T32 are monozygotic twins. Further DNA methylation data was collected from and additional two pairs of MZ twins with technical replication (samples with "C" prefixes - the three digits are pair number, individual number, and replicate number).
Bisulphite converted DNA was hybridised to the Illumina Infinium 450k Human Methylation Beadchip
Contributor(s) Gemma C, Ramagopalan SV, Down TA, Beyan H, Hawa MI, Holland ML, Hurd PJ, Giovannoni G, Leslie RD, Ebers GC, Rakyan VK
Citation(s) 23706135
Submission date Apr 18, 2013
Last update date Mar 22, 2019
Contact name Thomas A Down
Organization name University of Cambridge
Department WT/CRUK Gurdon Institute
Street address Tennis Court Road
City Cambridge
ZIP/Postal code CB2 1QN
Country United Kingdom
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (14)
GSM1125308 genomic DNA from CD14 B-cells, 1st pair 1st individual_T11 (BeadChip)
GSM1125309 genomic DNA from CD14 B-cells, 2nd pair, 1st individual_T21 (BeadChip)
GSM1125310 genomic DNA from CD14 B-cells, 2nd pair, 2nd individual_T22 (BeadChip)
This SubSeries is part of SuperSeries:
GSE46220 Inactive or moderately active human promoters are enriched for inter-individual epialleles
BioProject PRJNA198093

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
GSE46168_RAW.tar 183.1 Mb (http)(custom) TAR
GSE46168_TE_intensities.txt.gz 30.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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