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Series GSE36369 Query DataSets for GSE36369
Status Public on Jul 22, 2013
Title DNA methylation contributes to natural human variation
Platform organism Homo sapiens
Sample organisms Pan troglodytes; Homo sapiens; Pan troglodytes schweinfurthii; Pan troglodytes troglodytes; Pan troglodytes verus
Experiment type Methylation profiling by array
Third-party reanalysis
Summary 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.
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 (2010.3) Methylation module (1.8.5) software. Methylation score of each CpG is represented as beta value.
Contributor(s) Heyn HA, Salama SM, Esteller M
Citation(s) 23908385
Submission date Mar 08, 2012
Last update date Mar 18, 2020
Contact name Manel Esteller
Organization name IDIBELL
Department PEBC
Lab Cancer Epigenetics
Street address Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
City L'Hospitalet de Llobregat
State/province Barcelona
ZIP/Postal code 08908
Country Spain
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (322)
GSM924611 African American [GM17101]
GSM924612 African American [GM17102]
GSM924613 African American [GM17103]
Affiliated with GSM880123
Affiliated with GSM880152
Affiliated with GSM880000
Affiliated with GSM880003
Affiliated with GSM880005
Affiliated with GSM880009
Affiliated with GSM880014
Affiliated with GSM880020
Affiliated with GSM880023
Affiliated with GSM880025
Affiliated with GSM880026
Affiliated with GSM880029
Affiliated with GSM880030
Affiliated with GSM880034
Affiliated with GSM880038
Affiliated with GSM880039
Affiliated with GSM880042
Affiliated with GSM880058
Affiliated with GSM880066
Affiliated with GSM880075
Affiliated with GSM880086
Affiliated with GSM880092
Affiliated with GSM880118
Affiliated with GSM880129
Affiliated with GSM880138
Affiliated with GSM880139
Affiliated with GSM880141
Affiliated with GSM880143
Affiliated with GSM880144
Affiliated with GSM880151
Affiliated with GSM880156
Affiliated with GSM880157
Affiliated with GSM880159
Affiliated with GSM880166
Affiliated with GSM880168
Affiliated with GSM880169
Affiliated with GSM880170
Affiliated with GSM880171
Affiliated with GSM880172
Affiliated with GSM880176
Affiliated with GSM880177
Affiliated with GSM880178
Affiliated with GSM880180
Affiliated with GSM880181
Affiliated with GSM880182
Affiliated with GSM880185
BioProject PRJNA153243

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
GSE36369_AA-HC_validation.txt.gz 827 b (ftp)(http) TXT
GSE36369_NonEBV_SignalA_SignalB.txt.gz 173.6 Mb (ftp)(http) TXT
GSE36369_RAW.tar 183.1 Mb (http)(custom) TAR
GSE36369_Signal_A_Signal_B.txt.gz 1.1 Gb (ftp)(http) TXT
Processed data included within Sample table

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