|
| Status |
Public on Jun 01, 2013 |
| Title |
Pan troglodytes schweinfurthii A910 |
| Sample type |
genomic |
| |
|
| Source name |
blood
|
| Organism |
Pan troglodytes schweinfurthii |
| Characteristics |
gender: male
organism: Pan troglodytes schweinfurthii
tissue: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
unknown
|
| 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 standard recommended Illumina scanner protocol
|
| Description |
A910
|
| Data processing |
The methylation value was set to null for probes with a detection p-value < 0.01. A strict filtering step was performed to remove divergent probes based on the number and location of mismatches with their target site in each species genome assembly tested. We only retained those probes that had either a perfect match, or had 1 or 2 mismatches in the first 45bp but no mismatches in the 3' 5bp closest to the CpG site being assayed. Beta values from the autosomal probes and chromosome X probes were quantile normalized separately; additionally, chromosome X probes for male and female were quantile normalized separately.
|
| |
|
| Submission date |
Oct 23, 2012 |
| Last update date |
Jun 01, 2013 |
| Contact name |
Irene Hernando |
| E-mail(s) |
irene.hernando@upf.edu
|
| Organization name |
UPF/CSIC
|
| Street address |
Dr Aiguader 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE41782 |
A genome-wide comparative study of DNA methylation in great apes |
|
