The selected liver tissues were observed for gross changes, divided into pieces of about 0.1 g, snap-frozen directly in liquid nitrogen and stored at -80°C prior to RNA isolation for microarray analysis. The remaining livers were preserved in 10% phosphate-buffered formalin. The liver this website tissue fixed in neutral formalin was embedded in paraffin, sectioned, and stained with hematoxylin and eosin (H&E). Histopathologic
examinations of the liver sections were conducted by a pathologist and peer-reviewed. RNA extraction Frozen liver sections were ground in a Mixer Mill mm 200 (Retsch GmbH and Co. KG, Haan, Germany) using pre-cooled stainless steel balls. Total RNAs were isolated from livers with Trizol Reagent (Invitrogen, CA) using manufacturer recommended procedures. The ratio of the optical densities from RNA samples measured at 260 and 280 nm was used to evaluate nucleic acid purity, and total RNA concentrations were determined by the absorbance at 260 nm. The quality of total RNA was estimated based on the integrity of 28S and 18S rRNA. RNA was separated using 1% agarose gel electrophoresis. Good RNA quality was indicated by 28S rRNA banding having twice the intensity of the 18S rRNA, without significant smearing of the rRNA bands. Samples of total RNA from livers of rats from the same time points were pooled for subsequent use in the TSA HDAC Genechip analysis. Prior to GeneChip analysis, the pooled
total RNA samples were purified using the RNeasy Total RNA Mini Kit (Qiagen, Valencia, CA) GNS-1480 according GBA3 to manufacturer’s instructions. Oligo microarray hybridization Biotin-labeled cRNA samples were used for hybridization of Affymetrix GeneChip Rat 230 2.0 arrays. The arrays were prepared according to the protocol supplied with the GeneChip Sample Cleanup module (P/N 900371, Affymetrix Inc., Santa Clara, CA). Briefly, 5 μg total RNA was used for cDNA synthesis with the SuperScript Choice System (Invitrogen Life Technologies, Carlsbad, CA) employing a T7-(d7)24 primer.
After spin column purification, biotin-labeled cRNA was synthesized from the cDNA using the ENZO RNA Transcript Labeling Kit (Affymetrix Inc.). Spin column-purified cRNA was quality controlled using an Agilent 2100 Bioanalyzer and spectrophotometrically quantified. The cRNA (15 μg) was then fragmented in buffer supplied with the Cleanup Module and hybridized for 16 h at 45°C (Affymetrix Genechip Hybridization Oven 640). The microarrays were washed and stained with streptavidin-phycoerythrin (SAPE, Molecular Probes) on the Affymetrix Fluidics Station 450, including an amplification step according to the manufacturer’s instructions. Fluorescent images were read using the Gene Array Scanner 3000. The raw data image files (DAT) were converted into RPT files using Affymetrix Microarray Suite (MAS) 5.0. In RPT files, the scan data from the 36 pixels per oligo set were averaged.