|
Status |
Public on Feb 16, 2015 |
Title |
Blood-N09 |
Sample type |
genomic |
|
|
Source name |
prenatal tobacco exposure
|
Organism |
Homo sapiens |
Characteristics |
prenatal tobacco exposure: YES newborn gender: male tissue: Umbilical cord blood
|
Treatment protocol |
Umbilical cord blood was collected in EDTA-tubes, centrifuged to yield plasma, stored at -80ÂșC 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 |
N09
|
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 |
|