Gene expression analysis of peritoneal mesotheliomas following chemical treatment in F344 rats

This study was performed to characterize the gene expression profile of rat peritoneal mesothelioma (RPM) formation following treatment of Fischer 344 rats with o-nitrotoluene (o-NT) or bromochloracetic acid (BCA). Keywords: Rat, Mesotheliomas, Bromochloractetic acid, o-Nitrotoluene, Carcinogenesis, Microarray Four mesotheliomas from o-NT-treated rats and four mesotheliomas from BCA-treated rats were selected for microarray analysis. At necrosy, the tumors were collected, minced and flash frozen in liquid nitrogen. A non-transformed mesothelial cell line, Fred-PE (passage eight), was used as a source of reference RNA. Total RNAs from tumor tissue and Fred-PE were isolated with the RNeasy kit and 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol. For each two color comparison, 750 ng of each Cy3- and Cy5-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing and scanning with an Agilent Scanner. Data was obtained using the Agilent Feature Extraction software (v7.5), using default for all parameters. Two arrays for each comparison were used, incorporating a fluor reversal.