|
Status |
Public on Apr 01, 2013 |
Title |
cartilage knee 08121_OA |
Sample type |
genomic |
|
|
Source name |
cartilage knee
|
Organism |
Homo sapiens |
Characteristics |
disease state: osteoarthritis age: >60 years Sex: female haplogroup: J 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 |
osteoarthritic 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 |
|