microarrays according to their standard protocols. Briefly, cDNA was synthesized from 10 ug of RNA, labeled with Cy3, and hybridized to three replicate Nim bleGen S. cerevisiae 1 plex www.selleckchem.com/products/CP-690550.html 385K arrays for each RNA sample. Following washing and scanning of the arrays, data was extracted from the scanned image and analyzed for nor malized gene expression summary values by quantile normalization and the Robust Multi array Average algorithm using the NimbleScan software. ArrayStar 3. 0 software was used to analyze the expression data provided by NimbleGen. Mean TE4G and TEWT values were calculated for each gene from all nine microarray measurements of HP or T mRNA intensities obtained in the three biological replicates to obtain the log log plot in Figure 4.

To calculate mean TE4G TEWT ratios for the purpose of assigning standard errors to the values, the ratios were calculated separately for each project from the mean TE4G and mean TEWT values calculated from the three technical replicates for that project, and the resulting TE4G TEWT ratios for each project were averaged. The three mean TE4G and mean TEWT values determined in this way from projects I III were also used to conduct two tailed Students t tests of the significance of differences between mean TE4G and mean TEWT values for individual genes. Accession number The microarray data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus and are accessible through GEO Series accession num ber GSE25721 acc GSE25721.

Real time quantitative RT PCR analysis of polysomal mRNA distributions RNA samples from the WCE or gradient fractions con taining HP, LP, or 80S monosomes were isolated as pre viously described. The level of mRNA for each gene of interest relative to the amount of 18S rRNA was quantified by qRT PCR analysis. Briefly, cDNA was synthesized from 1 ug of RNA using SuperScript III First Strand Synthesis SuperMix according to the vendors recommended protocol. The synthesized first strand cDNA was diluted 1,10, and 2 ul of the diluted cDNA was used for subsequent real time PCR amplifica tion using the Stratagene MX3000P and Brilliant II SYBR Green QPCR Master Mix according to the vendors instructions. The primers used in qRT PCR ana lysis for the mRNAs analyzed in Figure 2 are listed in Table S2. The real time PCR reac tions were carried out in triplicate for each cDNA sample to obtain AV-951 average Ct values.

The amount of mRNA in a set of gradient fractions containing HP, LP or 80S species relative to its level in total RNA was determined by first calculating screening library 2 Ct, where Ct Ct norm Ct norm, Ct norm Ct GOI Ct 18S, and Ct norm Ct GOI Ct 18S. Ct GOI and Ct GOI are the Ct values determined for the gene of interest in the appropriate gradient fractions or total RNA, respectively, Ct 18S and Ct 18S are the corresponding values for 18S rRNA. The resulting 2 Ct values were then multiplied by a factor representing the proportion of the total A280 units in the gradient found in th