Supplementary Figure 2: Ezh2-deficient mature DCs display comparable H3K27me3 content and gene-expression profiles.
(a) The content of H3K27me3 of cultured bone marrow derived mature DCs (day 8) from poly(I)-poly(C) treated Ezh2f/f (solid line) and Ezh2f/f Mx1-Cre (Ezh2Δ/Δ) (dashed line) mice were analyzed by intracellular staining (H3K27me3) and flow cytometry. Isotype control is indicated by filled area. Gated mature DCs (CD11c+Class IIhi) are shown in these histograms. (b-d) Gene expression patterns in control and Ezh2-deficeint BMDCs. RNA isolated from control (Ezh2f/f) and Ezh2-deficient (Ezh2Δ/Δ) DCs were processed according to manufacturer’s instruction. Samples were hybridized to Illumina WG6v2 mouse arrays. Raw intensities were extracted using Bead Studio, and quantile normalized. Differential gene expressions were determined with limma, using BH multiple test correction and an FDR cutoff of ≤ 0.05. All data processing and analysis were performed using Accelrys Pipeline Pilot (www.accelrys.com). Biological triplicates were done for each group. (b) Venn diagram showing the overlap in differentially expressed genes (DEGs) between control dendritic cells with versus without LPS stimulation, and Ezh2-deficient DCs with versus without LPS stimulation. Control DC specific DEGs were 29 and Ezh2-deficient DC specific DEGs were 28. In total, 98% of the DEGs (2643) were in common between control and Ezh2-deficient DCs. (c) Scatter plot of log2, normalized intensities from the array of a representative experiment of bone marrow derived control versus Ezh2-deficient immature DCs (iDCs). A Pearson’s r correlation of 0.9947 was obtained. (d) Scatter plot of log2, normalized intensities from the array of a representative sample of control versus Ezh2-deficient LPS-stimulated mature DCs (mDCs). A Pearson’s r correlation of 0.9932 was obtained.
