|
| Status |
Public on Jul 19, 2011 |
| Title |
Vehicle_24hr_B96171_F_Bladder |
| Sample type |
RNA |
| |
|
| Source name |
Vehicle-treated, urinary bladder, 24hr
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
gender: female
tissue: urinary bladder
treatment: vehicle
treatment duration: 24hr
|
| Treatment protocol |
Rats (25/group) were assigned to groups receiving vehicle or 100 mg/kg of compound C1 by oral gavage (10 mL/kg). Five sets of 5 females/dose group received either a single dose on Day 1 with necropsy 4 to 5 hours post-dose; a single dose on Day 1 with necropsy on Day 2 (approximately 24 hours post-Day 1 dosing); 2 daily doses with necropsy on Day 3; 4 daily doses with necropsy on Day 5; or 7 daily doses with necropsy on Day 8.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from ~30 ug pieces of tissue according to the RNeasy extraction procedure (Qiagen, Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
1 ug of total RNA was reverse transcribed to double-stranded cDNA using the Bioarray Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences, Farmingdale, NY), and biotinylated cRNA was generated using the BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences, Farmingdale, NY).
|
| |
|
| Hybridization protocol |
10 ug of biotinylated cRNA spiked with hybridization controls (bioB, bioC, bioD and cre) was hybridized to an Affymetrix RAE 230 array.
|
| Scan protocol |
GeneChip Scanner 3000 (Affymetrix, Santa Clara, CA).
|
| Description |
48762
|
| Data processing |
Each tissue and time point was analyzed independently. Expression data was pre-processed using Rosetta Resolver (Rosetta Inpharmatics LLC, Seattle, WA). A probe set was considered present if the p-value associated with its intensity being different from the background intensity was ≤ 0.05. Probe sets with intensities that were not significantly different from the corresponding backround intensities were set to the background levels. Probe sets that were present on at least 5 microarrays out of 10 at each given time point were included for further analysis. The data was normalized using quantile normalization (Guatier et al., 2004) prior to further analysis.
|
| |
|
| Submission date |
Jan 28, 2011 |
| Last update date |
Jul 19, 2011 |
| Contact name |
Scott Taylor |
| E-mail(s) |
Scott.Taylor@Amgen.com
|
| Organization name |
Amgen Inc.
|
| Street address |
One Amgen Center Drive
|
| City |
Thousand Oaks |
| State/province |
CA |
| ZIP/Postal code |
91320-1799 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (1) |
| GSE26936 |
Expression data from rat urinary bladder and non-glandular stomach tissue samples |
|
