|
| Status |
Public on Feb 16, 2015 |
| Title |
Blood-N12 |
| Sample type |
genomic |
| |
|
| Source name |
prenatal tobacco exposure
|
| Organism |
Homo sapiens |
| Characteristics |
prenatal tobacco exposure: YES
newborn gender: female
tissue: Umbilical cord blood
|
| Treatment protocol |
Umbilical cord blood was collected in EDTA-tubes, centrifuged to yield plasma, stored at -80ºC and thawed before use.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from venous umbilical cord blood with the RealPure kit (REALPURE, REAL, DURVIZ, Ref: RBMEG01) and was quantified with the Nanodrop-2000C Spectrophotometer. A DNA quality check was performed with Quant-iT PicoGreen dsDNA reagent.
|
| Label |
Cy3, Cy5
|
| Label protocol |
Standard Illumina labelling protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
N12
|
| Data processing |
R-bioconductor/minfi
The non_normalized.txt contains unmethylated and methylated signal intensities. The beta values were obtained before raw data normalization; we used Subset-quantile Within Array Normalization (SWAN)(available in the minfi Bioconductor package).
|
| |
|
| Submission date |
Dec 18, 2014 |
| Last update date |
Feb 16, 2015 |
| Contact name |
Agustin F Fernandez |
| E-mail(s) |
affernandez@hca.es, agusff@gmail.com
|
| Phone |
985652411
|
| Organization name |
Oviedo University-HUCA
|
| Department |
IUOPA
|
| Lab |
Epigenetics
|
| Street address |
Avenida de Roma s/n
|
| City |
Oviedo |
| State/province |
Asturias |
| ZIP/Postal code |
33011 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE64316 |
DNA methylation patterns in newborns exposed to tobacco in utero |
|
