m. Animals had ad libitum access to food and acidified Cisplatin Sigma water. At 10 weeks of age, body weight was recorded and the mice were euthanized by cervical dislocation and perfused with RNase free DEPC treated PBS. Dis section procedures were started at 11,00 a. m. after a 4 hour period of food deprivation and were completed within a one hour time window. The Jackson Laboratory Animal Care and Use Committee approved the animal housing and experimental procedures described in this work. Inguinal fat pad, heart, liver, and both Inhibitors,Modulators,Libraries kidneys were dissected, cut into pieces not exceeding 0. 5 cm in any dimension, divided into two samples and placed in 15 ml conical tubes containing RNAlater solution. Each kidney sample consisted of one complete kidney, left or right. Tissues were homo genized in TRIzol reagent.
Total RNA was isolated by standard TRIzol methods according to the manufacturers protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instru ment and a RNA 6000 Nano LabChip assay. The RNA was treated with DNase1 according to Inhibitors,Modulators,Libraries the manufacturers methods. Microarray processing Illumina Sentrix Mouse 6 v1. 1 BeadChip processing Total RNA was reverse transcribed followed by second strand cDNA synthesis. For each sample, an in vitro transcription reaction was carried out incorporat ing biotinylated nucleotides according to the manufac Inhibitors,Modulators,Libraries turers protocol for Illumina Totalprep RNA amplification kit. 1. 5 ug biotin labelled cRNA was then hybridized onto Mouse 6 Expression Bead Chips for 16 hours at 55 C. Post hybridization staining and washing were performed according to manufacturers protocols.
Illu mina Sentrix Mouse 6 v1. 1 BeadChips were scanned using Illuminas BeadStation 500 scanner. Images were checked for grid alignment and then quantified using the BeadStudio software. Control summary graphs gen erated by BeadStudio were used as quality assurance tools for hybridization, washing stringency, and back ground. Integrity of Inhibitors,Modulators,Libraries the arrays was investigated using the BeadStudio array images and also using bead level image plots generated using the R beadarray package. Mean pixel intensities by bead type, were created using BeadStudio v3. 1 and processed with the R beadarray package. We performed the experiment in two blocks of three cages, separated by one month. Within each block, we assayed gene expression in each tissue using two Illumina Sentrix Mouse 6 v1.
1 BeadChips. Samples were randomly assigned to array positions within each chip with the constraint that sam ples from the same mouse were placed on separate chips. Quantile Inhibitors,Modulators,Libraries normalization was applied within each tissue, and sellekchem a correction for batch effects was applied separately for each gene using an MM regres sion estimator from the R robustbase software package. We selected 45905 probes which are mapped to 22869 genes based on the R illuminaMousev1p1BeadID. db package.