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Sample GSM1320508 Query DataSets for GSM1320508
Status Public on Jul 30, 2014
Title Before MOF supplementation_Subject3
Sample type genomic
Source name Blood
Organism Homo sapiens
Characteristics gender: Male
age: 30
cig/dag: 20
years of smoking: 15
pack years: 15
bmi: 18.3
tchol (mmol/l): 5.2
Treatment protocol PLoS One. 2011;6(12):e28460. doi: 10.1371/journal.pone.0028460
Extracted molecule genomic DNA
Extraction protocol gDNA from EDTA-treated blood was extracted by a DNeasy blood & tissue kit (Qiagen, Courtaboeuf, France)
Label Cy5 and Cy3
Label protocol See hyb protocol
Hybridization protocol Bisulphite converted DNA from the subjects was hybridized to the Illumina HumanMethylation450 BeadChip arrays. Briefly, 4 μg of bisulfite-converted DNA was isothermally amplified overnight (20–24 h) and fragmented enzymatically. Precipitated DNA was resuspended in hybridization buffer and dispensed onto the Infinium HumanMethylation450 BeadChips (12 samples/chip) using a Freedom EVO robot (Tecan). The hybridization procedure was performed at 48°C overnight (16–20 h) using an Illumina Hybridization oven. After hybridization, free DNA was washed away and the BeadChips were processed through a single nucleotide extension followed by immunohistochemistry staining using a Freedom EVO robot (Tecan).
Scan protocol The BeadChips were imaged using an Illumina iScan.
Description EDTA-blood sample
Data processing Detection p-values were calculated to identify failed probes as per Illumina's recommendations. Probes on sex chromosomes or containing SNPs (dbSNP v132) in the probe sequence were excluded. Raw data were normalized using Illumina's control probe scaling procedure and converted to methylation values on the 0–1 scale (M/(M + U + 100), where M and U represent the methylated and unmethylated signal intensities, respectively).
Submission date Feb 03, 2014
Last update date Jul 30, 2014
Contact name Celine BOBY
Organization name INRA
Street address Centre INRA Auvergne-Rhône-Alpes
City Saint Genes Champanelle
ZIP/Postal code 63122
Country France
Platform ID GPL13534
Series (2)
GSE54643 Dietary flavanols modulate the transcription of genes involved in cardiovascular pathology with complex changes of their DNA methylation state
GSE54690 Transcriptome-Methylome study of blood samples from flavanol diet intervention Paper title: Dietary flavanols modulate the transcription of genes associated with cardiovascular pathology and induces complex changes of their DNA methylation state.

Data table header descriptions
VALUE Average beta
Detection Pval

Data table
ID_REF VALUE Detection Pval
cg00050873 0.802581019 0
cg00212031 0.049983227 0
cg00213748 0.773715872 0
cg00214611 0.065018157 0
cg00455876 0.710966932 0
cg01707559 0.109878561 0
cg02004872 0.0396509 0
cg02011394 0.899860724 0
cg02050847 0.956482246 0
cg02233190 0.036781842 0
cg02494853 0.065467433 0
cg02839557 0.056786704 0
cg02842889 0.054330709 0
cg03052502 0.94621498 0
cg03155755 0.89512608 0
cg03244189 0.109116508 0
cg03443143 0.849229218 0
cg03683899 0.050537484 0
cg03695421 0.589291209 0
cg03706273 0.058640143 0

Total number of rows: 485512

Table truncated, full table size 11810 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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