|
| Status |
Public on Jan 08, 2014 |
| Title |
2w_dmm_2 |
| Sample type |
RNA |
| |
|
| Source name |
2 wks post-surgery_treated
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl6/J
Sex: male
age: 12 weeks
tissue: articular cartilage from medial tibial plateau
treatment: destabilisation of the medial meniscus (DMM)
time post surgery: 2 weeks
|
| Treatment protocol |
articular cartilage from the tibia plateaus of 8 knees was pooled in RNA Later and frozen. The pooled samples were thawed on ice RNA later removed and RLT buffer with 1% mercaptoethanol added. Samples disrupted with a scalpel and homogenised with a rotor stator 3 times for 10 seconds at a time, with a 5 second interval in between.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using QIAGEN micro kit with modifications. All samples were digested with Proteinase K for 30 minutes at 55 degrees C in RLT buffer prior to their application on the silica columns. RNA quality control was performed with agilent bioanalyser.
|
| Label |
biotin
|
| Label protocol |
Ovation Pico system was used to amplify the RNA (two rounds of SPIA amplification) and labeled with the FL-Ovatioon Biotin module V2. Quality control of amplified cDNA was performed with Agilent Bioanalyzer.
|
| |
|
| Hybridization protocol |
Labelled cDNA was hybridised to an Illumina Mouse WG-6 v2.0 Expression BeadChip following the manufacturer's protocol.
|
| Scan protocol |
Bead array reader was used to detect the Cy3 fluorescence emmision according to the manufacturers protocol.
|
| Description |
replicate 2
|
| Data processing |
Data were variance stabilised and quantile normalised using Lumi (v.2.8.0) in R (v.2.15.0). The detection p-value threshold was set to 0.01 (lumi default) and probes need to be successfully selected (p<0.01 in Lumi) in at least one sample to pass the selection.
|
| |
|
| Submission date |
Jan 07, 2014 |
| Last update date |
Jan 08, 2014 |
| Contact name |
Anastasios Chanalaris |
| E-mail(s) |
anastasios.chanalaris@kennedy.ox.ac.uk
|
| Organization name |
University of Oxford
|
| Department |
Kennedy Institute of Rheumatology
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7FY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6887 |
| Series (1) |
| GSE53857 |
Medial Tibial Plateau articular cartilage changes 2 ,4 and 8 weeks after DMM |
|
