The mixture was transferred to an RNeasy

spin column placed in a 2 ml collection tube. The flow-through was discarded after a 15 s centrifugation at 8000 × g. The column was washed with 700 μl of Buffer RW1 and then with 500 μl of Buffer RPE twice. Total RNA was eluted from the column with 30 μl of RNase-free water and quantified by spectrophotometer. Microarray analysis The Affymetrix GeneChip® RG-U34A, containing 8799 rat genes and EST sequences, was used for the microarray analysis. Briefly, 2.5 μg of total RNA from each rat was reversely transcribed, using the standard 3′IVT protocol as described previously [24], and hybridized to a GeneChip. A total of 12 GeneChips were used, four for each sample group from Normal, Dex, and Dex-Pc rats. The data were first analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis see more check details settings and global scaling as normalization method. The trimmed mean target intensity of

each array was arbitrarily set to 1000. Comparisons of global gene expression and identification of genes that were up- or down-regulated by dexamethasone treatment or by P. HSP targets carinii infection in AMs from the three different groups of rats (Normal, Dex, and Dex-Pc) were performed with the Partek Genomic Suite 6.4 Software (Partek Inc., St. Louis, MO). Identification of cellular functions affected by dexamethasone or Pneumocystis infection was achieved by using the Ingenuity Pathway Analysis (IPA) software (Ingenuity Systems Inc. Redwood City, CA). The microarray data generated in this study have been deposited in the Gene Expression Omnibus with the accession number GSE20149. Real-time RT-PCR Approximately 0.2 μg of each total AM RNA sample

was reversely transcribed to cDNA using the iScript cDNA synthesis kit (Bio-Rad, Hercules, CA) and random primers in a total reaction volume of 20 μl. The reaction mixtures were incubated at 25°C for 5 min, 42°C for 30 min, Elongation factor 2 kinase and 85°C for 5 min. Of this, 2 μl of each cDNA product was used for quantitative PCR analysis. Real-time RT-PCRs for various target genes were performed using the Assays-on-Demand™ gene expression kits. Each kit contained two unlabeled PCR primers and a FAM™-labeled TaqMan probe (Applied Biosystems, Foster City, CA). Since the expression of the ribosomal protein S8 (RPS8) is not affected by Pneumocystis infection, RPS8 mRNAs were assayed in an identical manner as an internal control as described previously [25]. Results Quality of microarray data Since each GeneChip contained 8799 probe sets, a total of 105,588 expression data points were generated from the twelve arrays. Principle component analysis (PCA) was first performed to examine the correlations among the data produced from different arrays. The results of the first three principal components, which included the variance of 83.