|
| Status |
Public on Jul 01, 2016 |
| Title |
knee1 |
| Sample type |
genomic |
| |
|
| Source name |
Osteoarthritic knee cartilage
|
| Organism |
Homo sapiens |
| Characteristics |
subject status: joint replacement patient
disease state: Osteoarthritic
gender: Female
age (yrs): 77
body mass index: 25.19531
joint: Knee
sample type: Cartilage specimen from joint replacement surgery
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The DNA was extracted using Phenol-Chloroform method following TRIzole treatment of the homogenized tissues.
|
| Label |
cy3, cy5
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation 450 Bead-Chip microarray
|
| Scan protocol |
Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting
|
| Description |
9934089033_R02C02
|
| Data processing |
R packages minfi (version 1.6.0) and minfiData (version 0.3.4)
Normalized beta value by beta-mixture quantile normalization (BMIQ) method
The non_normalized.txt contains unmethylated and methylated signal intensities
|
| |
|
| Submission date |
Sep 30, 2015 |
| Last update date |
Jul 01, 2016 |
| Contact name |
Guangju Zhai |
| E-mail(s) |
guangju.zhai@med.mun.ca
|
| Phone |
1 709 864 6683
|
| Organization name |
Memorial University of Newfoundland
|
| Department |
Genetics, Medicine
|
| Street address |
300 Prince Philip Drive
|
| City |
St. John's |
| State/province |
NL |
| ZIP/Postal code |
A1B 3V6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL13534 |
| Series (1) |
| GSE73626 |
Genome-wide DNA methylation study of hip and knee osteoarthritic and healthy cartilage reveals embryonic organ and skeletal system morphogenesis as major pathways involved in osteoarthritis |
|
