|
| Status |
Public on Mar 15, 2016 |
| Title |
cartilage, OA, pat1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
facet joint cartilage
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: OA
tissue: facet cartilage (pooled from 3 facet OA cartilage samples)
|
| Treatment protocol |
No treatment was performed for facet cartilage from patients with OA and lumbar disc herniation (control).
|
| Growth protocol |
There was no growth protocol. Fresh facet cartilage was immediately homogenized using liquid nitrogen and extracted RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Hy3
|
| Label protocol |
400 ng total RNA from both facet osteoarthritis cartilage and control cartilage was labeled with Hy fluorescent labels, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| Channel 2 |
| Source name |
reference RNA
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: reference RNA
|
| Treatment protocol |
No treatment was performed for facet cartilage from patients with OA and lumbar disc herniation (control).
|
| Growth protocol |
There was no growth protocol. Fresh facet cartilage was immediately homogenized using liquid nitrogen and extracted RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Mini kit (Qiagen) according to the manufacturer's instructions.
|
| Label |
Hy5
|
| Label protocol |
400 ng total RNA from both facet osteoarthritis cartilage and control cartilage was labeled with Hy fluorescent labels, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer.
|
| |
|
| |
| Hybridization protocol |
The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 7th gen (Exiqon, Denmark). The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).
|
| Scan protocol |
microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA)
|
| Description |
Facet cartilage was extracted from medial aspect of the facet joint for both facet osteoarthritis and control samples
The 1_Exiqon_*_S01.txt raw files represent Hy3 data and the 0_Exiqon_*_S01.txt raw files represent Hy5 data.
|
| Data processing |
The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.
Expression is reported as log2(Hy3/Hy5) ratios
|
| |
|
| Submission date |
Mar 15, 2016 |
| Last update date |
Mar 15, 2016 |
| Contact name |
Akihiro Nakamura |
| E-mail(s) |
ashmode930@gmail.com
|
| Organization name |
University Health Network
|
| Department |
Genetics and Development
|
| Street address |
60 Leonard Avenue
|
| City |
Toronto |
| ZIP/Postal code |
M5T2S8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL21599 |
| Series (1) |
| GSE79258 |
microRNA expression in facet cartilage degeneration |
|
