|
| Status |
Public on Dec 01, 2011 |
| Title |
EndothelialCells_High WSS_24hrs_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
endothelial cells exposed to 10Pa of shear stress for 24 hrs
|
| Organism |
Bos taurus |
| Characteristics |
tissue: aorta
cell type: endothelial cells (Ecs)
passage: P15
stress: 10Pa of shear stress
|
| Treatment protocol |
24 hrs before the flow experiments started culture media was changed and cells were allowed to equilibrate in flow media containing DMEM, 5% FBS, 1% pen/strep, and 8% Dextran 70. For treatment, cells were placed subjected to either 0,2 or 10Pa of shear stress by placement in a flow loop system in which media was circulated over the cells to produce the mentioned shear stress values. After 24 hours the experiment was ended and coverslips of cells removed from the chamber.
|
| Growth protocol |
Bovine Aortic Endothelial Cells were seeded on glass coverslips and allowed to grow to confluence for 5 days. Cells were maintained in DMEM with 10% FBS and 1% penicilin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted following Qiagen RNeasy Mini Kit protocol using spin column technology. Purity and integrity were confirmed.
|
| Label |
biotin
|
| Label protocol |
Conducted using Affymetrix standard protocols.
|
| |
|
| Hybridization protocol |
Standard protocol described in Affymetrix GeneChip 3' IVT Express Kit.
|
| Scan protocol |
Affymetrix GeneChip Scanner and software.
|
| Description |
High4
PMH4_1_(Bovine).CEL
|
| Data processing |
All analyses were performed in R/Bioconductor. Affymetrix bovine CEL files were preprocessed and normalized using RMA. Informative, valid probe sets were determined using FARMS (Tolloen et al., 2007, Bioinformatics 23:2897-2902). FARMS represents an unbiased approach to remove non-informative probe sets based on their intra-probe set correlation. Sample to sample data exploration was performed using unsupervised hierarchial clustering and principle component analysis. Differential gene expression analysis was performed using a linear model approach and employing an empirical Bayes method for calculation of statistical significance (Bioconductor,limma package). We identified those probe sets whose expression were significantly enriched or depleted by at least two fold change and statistically significant following 1% FDR adjustment of p-values.
|
| |
|
| Submission date |
May 18, 2011 |
| Last update date |
Dec 01, 2011 |
| Contact name |
Jennifer Dolan |
| E-mail(s) |
[email protected]
|
| Organization name |
University at Buffalo
|
| Department |
Neuroscience
|
| Street address |
3435 Main Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14214 |
| Country |
USA |
| |
|
| Platform ID |
GPL2112 |
| Series (1) |
| GSE29376 |
Endothelial Cells Express a Unique Transcriptional Profile under Very High Wall Shear Stress Known to Induce Expansive Arterial Remodeling |
|
