|
| Status |
Public on Feb 28, 2014 |
| Title |
wk12_DEN50__DEN_11 |
| Sample type |
RNA |
| |
|
| Source name |
rat liver, cirrhosis (DEN 50mg, week 12)
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
sex: male
tissue: liver
disease status: cirrhosis
|
| Treatment protocol |
Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg, 100mg/kg, or vehicle control (PBS) for 18 weeks. A subset of rats received either daily (5X a week) IP injections of 2 mg/kg erlotinib or vehicle control during weeks 13 - 18. In a separate study, the erlotinib dose was lowered to 0.5 mg/kg. The vehicle groups from the two studies were not significantly different so they were combined together for analysis. Rats were weighed at the end of each week. Animals were sacrificed at 9, 13 and 19 weeks after a one-week washout period to eliminate acute effects of DEN. At the time of sacrifice, the non-tumor liver tissues were collected in RNase-free tubes and snap-frozen in liquid nitrogen. Frozen tissues were stored at -80°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Using frozen non-tumor liver tissues, total RNA was extracted using TRIzol (Invitrogen).
|
| Label |
Cy5
|
| Label protocol |
Refer to the Illumina beadarray Assay System Manual
|
| |
|
| Hybridization protocol |
Refer to the Illumina beadarray Assay System Manual
|
| Scan protocol |
Refer to the Illumina beadarray Assay System Manual
|
| Description |
wk12_DEN50__DEN_11
|
| Data processing |
For each probe, replicate mesurements were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm using GenePattern IlluminaNormalizer module.
|
| |
|
| Submission date |
Nov 17, 2009 |
| Last update date |
Feb 28, 2014 |
| Contact name |
Yujin Hoshida |
| E-mail(s) |
Yujin.Hoshida@UTSouthwestern.edu
|
| Organization name |
University of Texas Southwestern Medical Center
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL6101 |
| Series (2) |
| GSE19057 |
Gene expression profile of liver tissue in low-dose, repeated diethylnitrosamine (DEN)-treated rat treated with erlotinib |
| GSE27641 |
EGFR inhibition prevents liver cirrhosis and hepatocellular carcinoma |
|
