|
| Status |
Public on Jul 22, 2013 |
| Title |
Chimpanzee [A958] |
| Sample type |
genomic |
| |
|
| Source name |
Blood
|
| Organism |
Pan troglodytes troglodytes |
| Characteristics |
gender: Female
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was quantified by Quant-iT PicoGreen dsDNA Reagent (Invitrogen) and the integrity was analyzed in a 1.3% agarose gel.
|
| 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 High Scan SQ using standard recommended Illumina scanner setting
|
| Description |
PBMC
|
| Data processing |
The methylation value was set to null for probes with a detection p-value >0.01. Probe sequences (50-mer oligonucleotides) were uniquely mapped to the reference chimpanzee genome Pan_troglodytes-2.1.4 using BWA. We retained only the autosomal probes with either a perfect match, or 1 mismatch in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Quantile normalization was performed on the pooled signals from color channels and average β-values were recalculated using Genome Studio V2011.2.
|
| |
|
| Submission date |
Oct 19, 2012 |
| Last update date |
Jul 22, 2013 |
| 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 |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE36369 |
DNA methylation contributes to natural human variation |
|
