E-GEOD-36369 - DNA methylation contributes to natural human variation

Status
Released on 22 July 2013, last updated on 29 July 2013
Organism
Homo sapiens, Pan troglodytes, Pan troglodytes schweinfurthii, Pan troglodytes troglodytes, Pan troglodytes verus
Samples (322)
Array (1)
Protocols (306)
Description
DNA methylation analysis using the Infinium HumanMethylation450 BeadChip platform (Illumina) of 96 Caucasian American, 96 Han Chinese American and 96 African American LCL samples determined differences in terms of differentially methylated sites. Importantly, the observed differences were confirmed in primary blood samples of 10 healthy Caucasian, 10 African American (GSE36064) and 10 Asian individuals. Genes associated to differentially methylated site suggest an influence of DNA methylation on phenotype differences. Interestingly, methylation differences could be partially traced back to genetic polymorphisms. 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 (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.
Experiment types
methylation profiling by array, unknown experiment type 
Contacts
Antonio Gómez <agomezm@idibell.cat>, Holger A Heyn, Manel Esteller, Sebastian M Salama
MIAME
PlatformsProtocolsFactorsProcessedRaw
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