|
| Status |
Public on Dec 18, 2008 |
| Title |
Rat17 LUSH 3D rep2 |
| Sample type |
RNA |
| |
|
| Source name |
lung tissue
|
| Organism |
Rattus norvegicus |
| Characteristics |
exposed to sustained hypoxia: 3D
|
| Treatment protocol |
Rats subject to the intermittent hypoxia (IH) treatment were exposed to 90 second cycles of 10% inspired oxygen followed by 90 seconds of 21% inspired oxygen for 12 hours of simulated daylight when rats sleep; for the remaining 12 hours during the night, the rats were exposed to 21% inspired oxygen. Rats subject to the sustained hypoxia (SH) treatment were exposed to 10% inspired oxygen at all times. Time sacrifices of these rats exposed to IH and SH respectively were performed on days 1, 3, 7, 14, and 30.
|
| Growth protocol |
Adult inbred Sprague-Dawley male rats (weights: 250-275g) were placed in chambers in which oxygen and carbon dioxide concentrations were carefully monitored and controlled.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
To prepare RNAs for microarray experiments and quantitative RT-PCRs, 1 ml per 50 mg of frozen lung tissues were homogenized in ice cold Trizol, and phase separated with Chlorophorm (0.2ml per 1ml Trisol reagent). The RNAs were precipitated from the aqueous phase using Isopropanol (0.5ml per 1ml Trisol). The RNA pallet then was washed with 75%Ethanol. Next the extracted RNAs were purified further using the RNeasy Mini Cleanup protocol (Qiagen 74104) according to the manufacturer’s recommendations. The quantities of RNAs were determined by OD measurements at 260nm, and their qualities were assessed by Agilent Bioanalyzer and by running the RNAs on formamide formaldehyde denaturing gels
|
| Label |
Cy5
|
| Label protocol |
Briefly, the RNAs extracted from whole lung tissue of each rat (mixed with spiked-in bacterial RNAs served as positive controls) were reverse transcribed into double stranded cDNAs; then the cDNAs were amplified into cRNAs by in vitro transcription. The cRNAs were labeled with a red (Cy5) fluorescent dye and hybridized to a CodeLink Bioarray which is presynthesized with probes.
|
| |
|
| Hybridization protocol |
According to standard CodeLink protocols; see details at http://www1.gelifesciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28281090525-B500%29?OpenDocument&hometitle=WebDocs
|
| Scan protocol |
Microarray slides were scanned using a GenePix Array Scanner. For details, see the protocol at http://www1.gelifesciences.com/APTRIX/upp00919.nsf/Content/WD%3ACodeLink+Gene+E%28281090525-B500%29?OpenDocument&hometitle=WebDocs
|
| Description |
LUSH3D14V
|
| Data processing |
The raw intensity values were normalized by the CyclicLoess normalization method as described in Wu W, et. al, BMC Bioinformatics. 2005 Dec 28;6:309. The data was also preprocessed and postprocessed using the protocol described in the same paper and the submitted paper.
|
| |
|
| Submission date |
Aug 06, 2007 |
| Last update date |
Aug 14, 2011 |
| Contact name |
Wei Wu |
| E-mail(s) |
[email protected]
|
| Phone |
412-647-3156
|
| Fax |
412-647-7875
|
| Organization name |
University of Pittsburgh
|
| Department |
Medicine/PACCM
|
| Street address |
MUH 628 NW, 3459 Fifth Ave
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15213 |
| Country |
USA |
| |
|
| Platform ID |
GPL2890 |
| Series (1) |
| GSE8705 |
Temporal effects of intermittent- and sustained hypoxia on gene expression patterns in rat lungs |
|
