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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/31195

Title: Differentially expressed genes after treatment with adriamycin in DMBA-induced rat breast tumors (GSE16231)
Authors: Granados Principal, Sergio
Ramírez Tortosa, María del Carmen
Quiles Morales, José Luis
Ramírez Tortosa, César Luis
Sánchez Rovira, Pedro
Camacho-Corencia, P.
Issue Date: 1-Jun-2009
Abstract: 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.
Description: [Organism] Rattus norvegicus
[Experiment type] Expression profiling by array
[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).
1. GSM399913 Breast tumor biopsy_adriamycin_07SE125. [Characteristics] strain: Sprague-Dawley gender: female age: 12 weeks tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 09I1 (basal)
2. GSM399914 Total breast tumor_ adriamycin _07SE140. [Characteristics strain: ]Sprague-Dawley gender: female age: 19 weeks tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice. treatment: adriamycin (1 mg/kg weight/week, for 6 weeks) through the lateral tail vein after trucut biopsy. sacrifice: 7th week post-biopsy sample: 09I1 (final)
3. GSM399915 Breast tumor biopsy_adriamycin_07SE126. [Characteristics] strain: Sprague-Dawley gender: female age: 12 weeks tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 11D2 (basal)
4. GSM399916 Total breast tumor_ adriamycin _07SE141. [Characteristics] strain: Sprague-Dawley gender: female age: 19 weeks tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice. treatment: adriamycin (1 mg/kg weight/week, for 6 weeks) through the lateral tail vein after trucut biopsy. sacrifice: 7th week post-biopsy sample: 11D2 (final)
5. GSM399949 Breast tumor biopsy_adriamycin_07SE127. [Characteristics] strain: Sprague-Dawley gender: female age: 12 weeks tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 12I1 (basal)
6. GSM399959 Total breast tumor_ adriamycin _07SE142. [Characteristics] strain: Sprague-Dawley gender: female age: 19 weeks tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice. treatment: adriamycin (1 mg/kg weight/week, for 6 weeks) through the lateral tail vein after trucut biopsy. sacrifice: 7th week post-biopsy sample: 12I1 (final)
7. GSM399960 Breast tumor biopsy_adriamycin_07SE128. [Characteristics] strain: Sprague-Dawley gender: female age: 12 weeks tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 29I1 (basal)
8. GSM399961 Total breast tumor_ adriamycin _07SE143. [Characteristics] strain: Sprague-Dawley gender: female age: 19 weeks tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice. treatment: adriamycin (1 mg/kg weight/week, for 6 weeks) through the lateral tail vein after trucut biopsy. sacrifice: 7th week post-biopsy sample: 29I1 (final)
9. GSM399980 Breast tumor biopsy_adriamycin_07SE129. [Characteristics] strain: Sprague-Dawley gender: female age: 12 weeks tissue: Breast tumor. Trucut Biopsy of breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene before treatment with adriamycin. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 43D1 (basal)
10. GSM399981 Total breast tumor_ adriamycin _07SE144. [Characteristics] strain: Sprague-Dawley gender: female age: 19 weeks tissue: Breast tumor. Breast tumor chemically induced with 7,12-dimethylbenz(a)anthracene at the moment of sacrifice. treatment: adriamycin (1 mg/kg weight/week, for 6 weeks) through the lateral tail vein after trucut biopsy. sacrifice: 7th week post-biopsy sample: 43D1 (final)
Keywords: Aminals
Chordates
Mammals
Nonhuman vertebrates
Rodents
Muridae
Rattus norvegicus
Dataset
URI: http://hdl.handle.net/10481/31195
Rights : Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License
Appears in Collections:Información complementaria de las Investigaciones (Datos en Bruto)

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GSM399913.CEL.gz1. Breast tumor biopsy_adriamycin_07SE1252.68 MBWinRAR 3.70View/Open
GSM399913.xlsx1. Breast tumor biopsy_adriamycin_07SE125516.61 kBMicrosoft Excel XMLView/Open
GSM399914.CEL.gz2. Total breast tumor_ adriamycin _07SE140 2.43 MBWinRAR 3.70View/Open
GSM399914.xlsx2. Total breast tumor_ adriamycin _07SE140 515.12 kBMicrosoft Excel XMLView/Open
GSM399915.CEL.gz3. Breast tumor biopsy_adriamycin_07SE1262.59 MBWinRAR 3.70View/Open
GSM399915.xlsx3. Breast tumor biopsy_adriamycin_07SE126515.52 kBMicrosoft Excel XMLView/Open
GSM399916.CEL.gz4. Total breast tumor_ adriamycin _07SE1412.64 MBWinRAR 3.70View/Open
GSM399916.xlsx4. Total breast tumor_ adriamycin _07SE141515.62 kBMicrosoft Excel XMLView/Open
GSM399949.CEL.gz5. Breast tumor biopsy_adriamycin_07SE1272.65 MBWinRAR 3.70View/Open
GSM399949.xlsx5. Breast tumor biopsy_adriamycin_07SE127514.47 kBMicrosoft Excel XMLView/Open
GSM399959.CEL.gz6. Total breast tumor_ adriamycin _07SE1422.63 MBWinRAR 3.70View/Open
GSM399959.xlsx6. Total breast tumor_ adriamycin _07SE142514.52 kBMicrosoft Excel XMLView/Open
GSM399960.CEL.gz7. Breast tumor biopsy_adriamycin_07SE1282.54 MBWinRAR 3.70View/Open
GSM399960.xlsx7. Breast tumor biopsy_adriamycin_07SE128514.14 kBMicrosoft Excel XMLView/Open
GSM399961.CEL.gz8. Total breast tumor_ adriamycin _07SE1432.56 MBWinRAR 3.70View/Open
GSM399961.xlsx8. Total breast tumor_ adriamycin _07SE143514.54 kBMicrosoft Excel XMLView/Open
GSM399980.CEL.gz9. Breast tumor biopsy_adriamycin_07SE1292.56 MBWinRAR 3.70View/Open
GSM399980.xlsx9. Breast tumor biopsy_adriamycin_07SE129514.43 kBMicrosoft Excel XMLView/Open
GSM399981.CEL.gz10. Total breast tumor_ adriamycin _07SE1442.54 MBWinRAR 3.70View/Open
GSM399981.xlsx10. Total breast tumor_ adriamycin _07SE144515.53 kBMicrosoft Excel XMLView/Open
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