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| Status |
Public on Jun 01, 2009 |
| Title |
Differentially expressed genes after treatment with adriamycin in DMBA-induced rat breast tumors |
| Organism |
Rattus norvegicus |
| Experiment type |
Expression profiling by array
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| Summary |
The aim of this study was to compare the gene expression profile changes of DMBA-induced rat breast tumors after treatment with adriamycin. 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 tumor biopsy samples prior to adriamycin treatment, and compared with matched tumor biopsy samples after completion of the adriamycin treatment schedule.
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| 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 and subsequently treated with adriamycin (1 mg/kg body weight/week for 6 weeks) intravenously through lateral tail vein. Gene expression analysis was performed in paired samples as follows: ADR final trucut tumor vs initial trucut tumor (ADR 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).
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| 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
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| Organization name |
University of Granada
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| Street address |
Avenida del Conocimiento
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| City |
Granada |
| ZIP/Postal code |
18071 |
| Country |
Spain |
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| Platforms (1) |
| GPL1355 |
[Rat230_2] Affymetrix Rat Genome 230 2.0 Array |
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| Samples (10)
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| GSM399913 |
Breast tumor biopsy_adriamycin_07SE125 |
| GSM399914 |
Total breast tumor_ adriamycin _07SE140 |
| GSM399915 |
Breast tumor biopsy_adriamycin_07SE126 |
| GSM399916 |
Total breast tumor_ adriamycin _07SE141 |
| GSM399949 |
Breast tumor biopsy_adriamycin_07SE127 |
| GSM399959 |
Total breast tumor_ adriamycin _07SE142 |
| GSM399960 |
Breast tumor biopsy_adriamycin_07SE128 |
| GSM399961 |
Total breast tumor_ adriamycin _07SE143 |
| GSM399980 |
Breast tumor biopsy_adriamycin_07SE129 |
| GSM399981 |
Total breast tumor_ adriamycin _07SE144 |
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| Relations |
| BioProject |
PRJNA115165 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE16231_RAW.tar |
25.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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