Fig. 1

High-throughput DNA methylation comparison between monocytes (MOs) and derived dendritic cells (DCs) and macrophages (MACs). a Scheme depicting the differentiation system. Peripheral blood MOs were either exposed to granulocyte macrophage colony-stimulating factor (GM-CSF) + interleukin 4 (IL-4) or GM-CSF only to generate immature DCs and MACs (iDCs and iMACs), respectively. Maturation of these two cell types to mDCs and mMACs was achieved following incubation with lipopolysaccharide (LPS). b Summary of the DNA methylation changes obtained when comparing MOs differentiating to iDCs and iMACs, and the maturation towards mDCs and mMACs. Number of CpG sites and genes displaying significant gain (hyper) or loss (hypo) of DNA methylation changes are shown. c Heatmap of three paired samples (D1, D2 and D3) of MOs and their derived iMACs, iDCs, mMACs and mDCs. The heatmap includes all CpG-containing probes displaying significant methylation changes (>2-fold or <0.5-fold change; p < 0.01 and false discovery rate < 0.05) (data in Additional file 2). A scale is shown at the bottom, wherein beta values (i.e. the ratio of the methylated probe intensity to the overall intensity) range from −3 (lower DNA methylation levels, blue) to +3 (higher methylation levels, red). d Venn diagram showing the degree of overlap of demethylated CpGs/genes between MO-to-iDC and MO-to-iMAC differentiation. e Distribution of demethylated CpGs among genomic regions [intergenic, promoter (1,500 and 200 upstream of the transcription start site (TSS), 5′ untranslated region (UTR), first exon, gene body, and 3′UTR)] for MO-to-iDC and MO-to-iMAC differentiation. The darker insets within each bar indicate the number of sites annotated as enhancers. f Gene ontology (GO) enrichment analysis of demethylated CpGs in differentiation to iMACs and iDCs showing the most important categories. g Technical validation of the array data by bisulfite pyrosequencing of modified DNA. Three groups of genes are represented: demethylated genes specific to iDC differentiation, demethylated genes specific to iMAC differentiation, and genes that are commonly demethylated in iDC and iMAC differentiation