|
| Status |
Public on Aug 25, 2009 |
| Title |
FL-00-2 |
| Sample type |
RNA |
| |
|
| Source name |
FL-00
|
| Organism |
Rattus norvegicus |
| Characteristics |
Tissue: kidney. Age: 12 weeks. Gender: male
|
| Treatment protocol |
Animals (12-14 weeks old) from each strain were randomly divided into three groups (8 rats per group). Animals from groups 1 and 2 were given 100 mg/kg body weight/day I3C by gastric gavage for 7 and 10 days, respectively. Control group 3 was gavaged with carrier (vegetable oil).
|
| Growth protocol |
All rats were housed individually, given free access to water and standard commercial rat chow (Special Diet Services, Witham, Essex, UK), and maintained under controlled conditions of temperature (21±1°C) and humidity (50±10%), under a 12 hr light/dark cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was further purified by Dnase treatment and Rneasy Mini kit (Qiagen, UK).
|
| Label |
biotin
|
| Label protocol |
Biotin-labeled targets for the microarray experiment were prepared using 1µg of total RNA. Ribosomal RNA was removed with the RiboMinus Human/Mouse Transcriptome Isolation kit (Invitrogen), and cDNA was synthesized using the GeneChip® WT (Whole Transcript) Sense Target Labeling and Control Reagents kit as described by the manufacturer (Affymetrix, Santa Clara, CA, USA).
|
| |
|
| Hybridization protocol |
Hybridization was performed using 5 micrograms of biotinylated target, which was incubated with the GeneChip® Rat Exon 1.0 ST array (Affymetrix) at 45oC for 16 h. After hybridization, non-specifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
Arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and .CEL intensity files were produced using GeneChip Operating Software version 1.4 (Affymetrix).
|
| Description |
ATB2008021310Aaa.CEL
|
| Data processing |
Data were processed using OneChannelGUI in Bioconductor. The core set of probes was used and RMA was used to normlise the data. Limma was used to detect differentially exprressed genes.
|
| |
|
| Submission date |
Sep 04, 2008 |
| Last update date |
Jan 04, 2012 |
| Contact name |
Donald Dunbar |
| E-mail(s) |
donald.dunbar@ed.ac.uk
|
| Phone |
+44 131 242 6700
|
| Organization name |
University of Edinburgh
|
| Department |
Centre for Cardiovascular Science
|
| Lab |
Bioinformatics
|
| Street address |
47 Little France Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH16 4TJ |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL6543 |
| Series (2) |
| GSE12670 |
Renal gene expression analysis: transcript-level data |
| GSE12672 |
Renal gene expression analysis of rat malignant hypertensive end-organ damage |
|
