|
| Status |
Public on Jun 01, 2009 |
| Title |
Gene expression profile in a DMBA-induced rat breast tumor: biopsy vs total tumor |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
|
| Summary |
The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors from an initial stage to the moment of sacrifice. To this end, a cDNA microarray was performed (Affymetrix’s Rat Genome 230 2.0 array). This gene expression study was carried out on the umor biopsy samples and compared with matched tumor biopsy samples once the study ended (7 weeks after initial biopsy).
|
| |
|
| Overall design |
Breast tumors were induced with a single oral dosage of 7,12-dimethylbenz(alpha)anthracene (100 mg/kg body weight) in female Sprague-Dawley rats. Gene expression analysis was performed in paired samples as follows: DMBA final trucut tumor vs initial trucut tumor (DMBA final vs basal). For this assay, 5 samples were chosen according to histopathologic criteria (Bloom-Richardson grade II). Gene expression profiling was carried out using Affymetrix’s GeneChip technology, using the Rat Genome 230 2.0 array from this provider. All the protocols and apparatus were recommended by Affymetrix. Total RNA from frozen mammary tumors was extracted by RNeasy Mini kit and homogenized by QIAshredder columns according to manufacturer’s instructions. The quality and quantity of the obtained RNA was checked out through agarose electrophoresis and later spectrophotometry at 260/280 nm. Biotinylated cRNA was synthesized following the IVT labeling kit from Affymetrix and purified by the GeneChip Sample Cleanup Module from Affymetrix. The quality and quantity of the obtained cRNA was again checked out through agarose electrophoresis and posterior spectrophotometry at 260/280 nm. After hybridization, slides were washed and scanned following the manufacturer’s standard protocol. Intensity values were normalized by Robust Multichip Average method and subsequently these were filtered to remove the control sequences and those with a hybridization signal close to background. The spike controls were: BioB, BioC, BioD and Cre; because BioB was the least abundant in the samples, it was used to estimate the sensitivity of the experiment. The housekeeping control was GAPDH. After non-supervised clustering using Pearson correlation coefficient, statistical significance of gene expression was estimated by Student’s T test for paired samples, using GeneSpring GX 7.3 software (Agilent).
|
| |
|
| Contributor(s) |
Granados Principal S, Ramírez Tortosa MC, Quiles JL, Ramírez Tortosa CL, Sanchez Rovira P, Camacho Corencia P |
| Citation(s) |
21120994 |
| |
| Submission date |
May 26, 2009 |
| Last update date |
Jul 31, 2017 |
| Contact name |
Sergio Granados |
| E-mail(s) |
sergiogp@ugr.es
|
| Organization name |
University of Granada
|
| Street address |
Avenida del Conocimiento
|
| City |
Granada |
| ZIP/Postal code |
18071 |
| Country |
Spain |
| |
|
| Platforms (1) |
| GPL1355 |
[Rat230_2] Affymetrix Rat Genome 230 2.0 Array |
|
| Samples (10)
|
|
| Relations |
| BioProject |
PRJNA115167 |
Less...
More...