Supplemental Experimental Procedures RNA Isolation, Probe Preparation, Microarray Hybridization, Image Analysis, and Data Analysis Total RNA was isolated from peripheral T cells using TRIzol (Gibco-BRL). Quality of RNA was ensured

before labeling by analyzing 20–50 ng of each sample using the RNA 6000 NanoAssay and a Bioanalyzer 2100 (Agilent). Samples with a 28S/18S ribosomal peak ratio of 1.8–2.0 were considered suitable for labeling. For samples meeting this standard, 2 µg of total RNA was used for cDNA synthesis using an oligo(dT)-T7 primer and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen). Synthesis, linear amplification, and labeling of cRNA were accomplished by transcription in vitro using the MessageAmp aRNA Kit (Ambion) and biotinylated nucleotides (Enzo Diagnostics). Ten micrograms of labeled and fragmented cRNA were then hybridized to the mouse genome MOE430A array (Affymetrix), which contains ~22,000 oligonucleotide-based for ~14,000 well-characterized genes, at 45°C for 16 h. Automated washing and staining were performed using the Affymetrix Fluidics Station 400 according to the manufacturer's protocols. Finally, chips were scanned with a high-numerical Aperture and flying objective (FOL) lens in the GS3000 scanner (Affymetrix). Raw expression data were analyzed using Microarray Analysis 5.1 software (Affymetrix). Data were normalized to a target intensity of 500 to account for differences in global chip intensity. We utilized the Genespring 6.2 (Silicon Genetics) software package to identify genes differentially expressed between Ezh2fl/fl and Ezh2-/- samples using a parametric test with filtering (p-values <0.05) o