|
| Status |
Public on Mar 31, 2009 |
| Title |
Endothelial_mediumShear_rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Right iliac arterial endothelial cells exposed to medium shear
|
| Organism |
Sus scrofa |
| Characteristics |
Right iliac from Animal No. 1
|
| Growth protocol |
Reference endothelial cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Micro kit following manufacturer's protocol
|
| Label |
Cy5
|
| Label protocol |
Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion). 20 ng of total RNA for each sample, two rounds of amplification were performed, and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes, and reference RNA sample was labeled with Cy3 dyes.
|
| |
|
| Channel 2 |
| Source name |
Pooled referece RNA
|
| Organism |
Sus scrofa |
| Characteristics |
cultured porcine aortic endothelial cells
|
| Growth protocol |
Reference endothelial cells were grown in M199 supplemented with antibiotic/mycotic, FBS, and porcine serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Micro kit following manufacturer's protocol
|
| Label |
Cy3
|
| Label protocol |
Messenger RNA was amplified using a MessageAmp II aRNA amplification kit (Ambion). 20 ng of total RNA for each sample, two rounds of amplification were performed, and aminoallyl-UTP was used in the final round to provide reactive groups for dye incorporation. The RNA samples were labeled with Cy5 dyes, and reference RNA sample was labeled with Cy3 dyes.
|
| |
|
| |
| Hybridization protocol |
• Make hybridization buffer fresh each time. • Add 38 ul hybridization buffer to 12 ul fragmented Cy Dye labeled aa-aRNA. • Add 1ul each poly dA and appropriate Cot-1 DNA. • Heat at 95ºC for 2 minutes and put on ice to cool down. • Mix well and load sample to the array slide with lifter cover slip. • Hybridize overnight in 42ºC water bath.
|
| Scan protocol |
Scanned by GenePix 4000B and quantified using GenePix software
|
| Description |
Endothelial_mediumShear_rep2
|
| Data processing |
LOWESS normalized, include genes with signal in at least 16 of the 32 arrays, Agilent GeneSpring GX was used.
|
| |
|
| Submission date |
Feb 29, 2008 |
| Last update date |
Dec 23, 2008 |
| Contact name |
Ji Zhang |
| E-mail(s) |
ji.z@duke.edu
|
| Phone |
919-660-5125
|
| Fax |
919-684-4488
|
| Organization name |
Duke University
|
| Department |
Department of Biomedical Engineering
|
| Lab |
Cardiovascular simulations
|
| Street address |
Room 136 Hudson Hall
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL3461 |
| Series (1) |
| GSE10671 |
Endothelial Gene Expression in Regions of Defined Shear Exposure in the Porcine Iliac Arteries |
|
