|
| Status |
Public on Jul 10, 2015 |
| Title |
Corrected Sample 3 |
| Sample type |
RNA |
| |
|
| Source name |
4 mm aortic ring from thoracic aorta, 32wks, replicate 3
|
| Organism |
Oryctolagus cuniculus |
| Characteristics |
strain: New Zealand white
tissue: aorta
gender: male
age: 32 weeks
|
| Treatment protocol |
A 20 mmHg BP gradient was imposed using silk (permanent) or Vicryl (degradable) suture to mimic untreated CoA and surgically corrected CoA, respectively. Rabbits develop a pronounced stenosis and accompanying elevated BP as a stimulus for arterial remodeling within one week. Degradation of Vicryl suture in the corrected group restores aortic diameter close to normal, but with modest residual narrowing. Non-experimental rabbits were designated as a control group. This results in a statistically significant increase in mean, systolic and pulse BP proximal to the coarctation for CoA as compared to both control and corrected rabbits.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Sample labeling and hybridization were performed using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol.
|
| Label |
Cy3
|
| Label protocol |
Total RNA from each sample was linearly amplified and labeled with Cy3-UTP. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.
|
| |
|
| Hybridization protocol |
1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × blocking agent and 2.2 μl of 25 × fragmentation buffer, then heated at 60 °C for 30 min, and 55 μl 2 × GE buffer was added to dilute the labeled cRNA. 100μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.
|
| Scan protocol |
Hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (model G2505C).
|
| Description |
This sample displayed a different distribution of intensities compared to all other arrays and was therefore excluded from the analysis.
Gene expression at 32 wks of age
4 mm aortic ring
|
| Data processing |
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software (Agilent Technologies). Probes for which at least 8 out of 12 samples had flags in Detected (“All Targets Value”) were then chosen for further data analysis.
Differentially expressed probes with statistical significance were identified through Volcano Plot filtering. Finally, hierarchical clustering was performed to show the distinguishable gene expression profiling among samples.
|
| |
|
| Submission date |
Jul 09, 2015 |
| Last update date |
Jul 10, 2015 |
| Contact name |
John LaDisa |
| E-mail(s) |
john.ladisa@marquette.edu
|
| Phone |
414-288-6739
|
| Organization name |
Marquette University
|
| Department |
Biomedical Engineering
|
| Lab |
CV T.E.C. and MARVL
|
| Street address |
1637 West Wisconsin Ave
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53233 |
| Country |
USA |
| |
|
| Platform ID |
GPL13288 |
| Series (1) |
| GSE70687 |
Gene expression in experimental aortic coarctation and repair: candidate genes for therapeutic intervention? |
|
