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Please use this identifier to cite or link to this item: http://hdl.handle.net/10481/31633

Title: Gene expression profile in a DMBA-induced rat breast tumor: biopsy vs total tumor (GSE16232)
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 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).
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. 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).
[Platforms (1)] GPL1355 [Rat230_2] Affymetrix Rat Genome 230 2.0 Array
[Relations] BioProject PRJNA115167
1. GSM398893 Breast tumor biopsy_DMBA_07SE115. [Source name] Breast tumor biopsy, DMBA, basal moment. [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. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 31D3 (basal)
2. GSM398894 Total breast tumor_DMBA_07SE130. [Source name] Total breast tumor, DMBA, final moment. [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: none sample: 31D3 (final)
3. GSM399028 Breast tumor biopsy_DMBA_07SE116. [Source name] Breast tumor biopsy, DMBA, basal moment. [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. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 32D1 (basal).
4. GSM399030 Total breast tumor_DMBA_07SE131. [Source name] Total breast tumor, DMBA, final moment. [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: none sample: 32D1 (final)
5. GSM399430 Breast tumor biopsy_DMBA_07SE117. [Source name] Breast tumor biopsy, DMBA, basal moment. [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. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 37I1 (basal)
6. GSM399433 Total breast tumor_DMBA_07SE132. [Source name] Total breast tumor, DMBA, final moment. [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: none sample: 37I1 (final)
7. GSM399434 Breast tumor biopsy_DMBA_07SE118. [Source name] Breast tumor biopsy, DMBA, basal moment. [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. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 50I1 (basal)
8. GSM399456 Total breast tumor_DMBA_07SE133. [Source name] Total breast tumor, DMBA, final moment. [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: none sample: 50I1 (final)
9. GSM399460 Breast tumor biopsy_DMBA_07SE119. [Source name] Breast tumor biopsy, DMBA, basal moment. [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. Such biopsy was taken when tumor had 2cm3 volume. biopsy dimensions: 0.7 cm x 2.5 mm treatment: none sample: 52I4 (basal)
10. GSM399466 Total breast tumor_DMBA_07SE134. [Source name] Total breast tumor, DMBA, final moment. [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: none sample: 52I4(final)
Keywords: Animals
Chordates
Mammals
Nonhuman vertebrates
Rodents
Muridae
Rattus norvegicus
Dataset
URI: http://hdl.handle.net/10481/31633
Rights : Creative Commons Attribution-NonCommercial-NoDerivs 3.0 License
Appears in Collections:Información complementaria de las Investigaciones (Datos en Bruto)

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GSM398893.xlsBreast tumor biopsy_DMBA_07SE1151.93 MBMicrosoft ExcelView/Open
GSM398894.xlsTotal breast tumor_DMBA_07SE1301.93 MBMicrosoft ExcelView/Open
GSM399028.xlsBreast tumor biopsy_DMBA_07SE1161.93 MBMicrosoft ExcelView/Open
GSM399030.xlsTotal breast tumor_DMBA_07SE1311.93 MBMicrosoft ExcelView/Open
GSM399430.xlsBreast tumor biopsy_DMBA_07SE1171.93 MBMicrosoft ExcelView/Open
GSM399433.xlsTotal breast tumor_DMBA_07SE1321.93 MBMicrosoft ExcelView/Open
GSM399434.xlsBreast tumor biopsy_DMBA_07SE1181.93 MBMicrosoft ExcelView/Open
GSM399456.xlsTotal breast tumor_DMBA_07SE1331.93 MBMicrosoft ExcelView/Open
GSM399460.xlsBreast tumor biopsy_DMBA_07SE1191.93 MBMicrosoft ExcelView/Open
GSM399466.xlsTotal breast tumor_DMBA_07SE1341.93 MBMicrosoft ExcelView/Open
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