|
| Status |
Public on Apr 01, 2013 |
| Title |
cartilage knee 08664_N |
| Sample type |
genomic |
| |
|
| Source name |
cartilage knee
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: normal
age: <50 years
Sex: male
haplogroup: H
tissue: knee cartilage
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA was isolated using a home-made CTAB and chloroform-based method after breaking up the cartilage.
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA using EZ DNA Methylation kit (Zimo Research) was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using HiScan using standard recommended Illumina scanner setting
|
| Description |
normal cartilage knee sample
|
| Data processing |
Signal intensities were processed using methylumi and lumi R packages (R/Bioconductor). Methylumi R package with methylumIDAT function in order to obtain intensity signals, then transformed in a methyLumiM object, quantile color balance was adjusted and data were normalized using ssn procedure, obtaining as result M values.
|
| |
|
| Submission date |
Jan 03, 2013 |
| Last update date |
Apr 01, 2013 |
| Contact name |
Juan Fernandez Tajes |
| E-mail(s) |
jfernandezt@udc.es
|
| Organization name |
INIBIC
|
| Department |
Genomics Area
|
| Street address |
As Xubias
|
| City |
A Coruña |
| ZIP/Postal code |
15006 |
| Country |
Spain |
| |
|
| Platform ID |
GPL8490 |
| Series (2) |
| GSE43269 |
Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients (methylation) |
| GSE43270 |
Genome wide-DNA methylation analysis of articular chondrocytes reveals a cluster of osteoarthritic patients |
|
