|
| Status |
Public on Jul 30, 2014 |
| Title |
After 8wk 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. |
|
