|
| Status |
Public on Apr 30, 2019 |
| Title |
control_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
rat lung tissue, retrieved immediately after anesthesia and sacrifice
|
| Organism |
Rattus norvegicus |
| Characteristics |
Sprague-Dawley rat, male
|
| Biomaterial provider |
Charles River Laboratories
|
| Treatment protocol |
Anesthetized ventilated male Sprague-Dawley rats underwent tracheotomy for mechanical ventilation, then left thoracotomy and left lung hilar clamping for two hours, then the left lungs were reperfused and ventilated for 30 minutes (n=3) or 3 hours (n=3). Both the right and left lungs were retrieved for RNA extraction. RNA retrieved from lungs of six rats retrieved immediately after sacrifice served as controls.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from frozen lung specimens was performed according to the manufacturer's instructions
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA. A custom cDNA kit from Life Technologies was used with a T7-(dT)24 primer for this reaction.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 ug of cRNA were hybridized for 16 hr on RAE 230A Affymetrix arrays in the GeneChip Fluidics Station 400 and washed and scanned with a Hewlett Packard GeneArray Scanner. During the washing, the cRNA probe was labeled with R-Phycoerythrin streptavidin.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
rat lung control rep4
|
| Data processing |
Affymetrix GeneChip Microarray Suite 5.0 software was used for washing, scanning, and basic analysis. Analysis of microarray data was performed using GeneSpring software 7.2. A cross gene error model was employed to set a cut off value for normalization. Analysis of variance (ANOVA) was performed with Benjamini and Hochberg false discovery rate (FDR) of 5%.
|
| |
|
| Submission date |
Nov 16, 2007 |
| Last update date |
Apr 30, 2019 |
| Contact name |
Thomas Michael Egan |
| E-mail(s) |
ltxtme@med.unc.edu
|
| Phone |
919 966-3381
|
| Fax |
919 966-3475
|
| Organization name |
University of North Carolina
|
| Department |
Surgery
|
| Lab |
CT Surgery
|
| Street address |
Med Schol Wing C Room 354
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7065 |
| Country |
USA |
| |
|
| Platform ID |
GPL341 |
| Series (1) |
| GSE9634 |
Gene Expression Changes due to Rat Lung Ischemia-Reperfusion Injury |
|
