Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from rat orthotopic bladder cancer

ABSTRACT: In the development and progression of bladder cancer, there are many genetic changes. We established a SD rat orthotopic bladder cancer model through intravesical instillation of N-methyl-nitrosourea and pathologic diagnosis is bladder transtional cell carcinomal (BTCC). We used microarrays to analysis the gene expression changes among these rat bladder carcinoma, adjacent normal tissues and bladder tissues of normal rats. Three paired tumor tissues (Group A) and adjacent normal tissues (Group B) were obtained from 3 SD rats with BTCC, and 3 normal tissues (Group C) obtained from 3 normal SD rats. Affymetrix microarrays analyzed the gene expression changes among above 3 groups of tissues.

ORGANISM(S): Rattus norvegicus

SUBMITTER: Chun-Wu Pan

PROVIDER: E-GEOD-76702 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Gastric cancer (GC) is one of the most common cancer worldwide. Specific and reliable molecular markers are limited; it is critical to identify new biomarkers for GC to aid in early diagnosis, treatment strategy, and prognosis evaluation. Microarray technology makes it possible to measure the expression levels of thousands of genes, and identifying meaningful and useful molecular targets from these large data. Total RNA was extracted from 10 pairs of GC tissue and adjacent non-tumor mucosa using TRIzolÂ® reagent (Invitrogen, Carlsbad, CA, US) following the manufacturer's instructions. The RNA integrity number (RIN), detected by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US), was used to determine the RNA integrity. Total RNA meeting the specified quality criteria (RIN â¥ 7.0 and 28S/18S â¥ 0.7) were further purified using an RNase-Free DNase Set (Qiagen, Hilden, Germany) and an RNeasyÂ® Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Purified total RNA was then used for obtaining biotin-labeled cRNA by applying the GeneChipÂ® 3'IVT Express Kit (Affymetrix, Santa Clara, CA, US), according to the manufacturer's instructions. Then, the GeneChipÂ® Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, US) was used for performing the array hybridization and wash, with the use of a GeneChipÂ® Hybridization Oven 645 (Affymetrix, Santa Clara, CA, US) and a GeneChipÂ® Fluidics Station 450 (Affymetrix, Santa Clara, CA, US). All arrays were scanned using a GeneChipÂ® Scanner 3000 (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with the default settings. Raw data were normalized by the MAS 5.0 algorithm in GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). The significance analysis of microarray (SAM) was used to identify genes that were differentially expressed between the GC and normal tissues. Genes were considered to be differentially expressed when the Tumor versus Normal signal log ratio values were â¥2 or â¤0.5.

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Expression data from rat orthotopic bladder cancer

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