|
| Status |
Public on Jul 10, 2007 |
| Title |
OA 3 |
| Sample type |
RNA |
| |
|
| Source name |
Knee articular cartilage, 4 weeks following OA surgery
|
| Organism |
Rattus norvegicus |
| Characteristics |
Strain: Sprague-Dawley, Gender: male, Weight: 350 g
|
| Treatment protocol |
OA Surgery: ACL transection and partial medial meniscectomy; Exercise protocol: 30 minutes walking on rotating cylinder 3x per week
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tissue dissection and immediate immersion/homogenization in TRIzol. Aqueous phase transferred to QIAgen RNeasy Mini column for RNA prep.
|
| Label |
Affymetrix Hyb/Wash/Stain Kit
|
| Label protocol |
See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.
|
| |
|
| Hybridization protocol |
See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Fluidics Station 450.
|
| Scan protocol |
See Affymetrix GeneChip® Expression Analysis Technical Manual. Used the GeneChip® Scanner 3000 with Workstation.
|
| Description |
Samples underwent 2 rounds of amplification prior to labeling using the Affymetrix GeneChip® Two-Cycle cDNA Synthesis Kit.
|
| Data processing |
Raw data gene expression files from Affymetrix GeneChips were imported into GeneSpring, version 7.2, software (Silicon Genetics, Redwood City, CA). GC-robust multichip analysis preprocessing was performed. Raw data transformation set values <0.01 at 0.01, per-chip normalization was set at the 50th percentile, and per-gene normalization was set to the median and to values in control/sham samples. Data sets from sham-operated samples were assigned to the normal treatment group, and thus defined baseline expression for each probe. The remaining data sets (samples from contralateral and ipsilateral joints) were assigned to diseased treatment groups, averaged, and used in subsequent analysis. All data were interpreted using the log-ratio setting. From the starting list of 31,099 probes, 17,597 probes were determined to have a reliable signal, using the GeneSpring 7.2 SG1a-1 signal intensity quality control script. The script was adjusted to require signal intensity above a threshold of 50 in 2 of the 3 conditions. The data were then passed through a parametric Welch one-way analysis of variance (ANOVA) script, with P values less than 0.05 considered significant, which reduced the list to 3,877 probes. Post hoc Bonferroni multiple comparison testing was performed to identify statistically significant changes in expression between sham-operated samples and contralateral samples, and between sham-operated samples and ipsilateral samples, with P values less than 0.05 considered significant.
|
| |
|
| Submission date |
Jun 11, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Tom Appleton |
| E-mail(s) |
[email protected]
|
| Organization name |
The University of Western Ontario
|
| Department |
Physiology & Pharmacology
|
| Lab |
Frank Beier
|
| Street address |
Rm 0061 DSB The University of Western Ontario
|
| City |
London |
| State/province |
ON |
| ZIP/Postal code |
N6A5C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE8077 |
Global analyses of gene expression in early experimental knee osteoarthritis |
|
