Dendritic cell (DC) lineages coordinate immune system activity through functional specialization. • Irf4, a transcription factor(TF), is required for CD11b+ DC lineage development from bone marrow stem cells and has been implicated in multiple inflammatory diseases, eg. asthma. • The epigenetic consequences of immune specialization in CD11b+ DCs and relation to inflammatory diseases remain largely unexplored partly due to the difficulty of using highly purified, and typically, limited populations of cells in ChIP-seq (chromatin immunoprecipitation then sequencing) assays. • A robust, multiplexed ChIP-seq protocol – using an input control, TF (CTCF) and histone modification marks (H3K9me3- methylation, H3K27ac-acetylation) - was developed using limited amounts of K562 cells, for the Ion ProtonTM system. • Peak-calling analysis was performed using using MACS2. • Significant data correlations were observed with ENCODE. • The Ion ProtonTM results are based on chromatin derived from 1 million(M) cells, making it viable for generating data from a limited number of primary cells. This is in contrast to the 10M cells recommended by ENCODE. • The developed methodology was used to compare Irf4 genomic binding sites generated from flow-sorted populations of 1, 3, 5, and 20M CD11b+ lineage murine DCs. • Comparable Irf4 ChIP-seq results were obtained from 5M versus 20M cells, indicating that as low as 5M flow-sorted cells can be used to acquire high quality(FDR: 10-19) data. • We identified genomic Irf4 binding sites proximal to genes, whose activity is consistent with CD11b+ DC lineage activity and/or known to contribute to inflammatory disease. • We examined Irf4 functional regulation of the identified gene targets via RNA-seq analysis with CD11b+ DCs and a related lineage, CD103+ DCs. Integrating expression analysis with ChIP-seq indicates a unique CD11b+ DC gene expression program concordant with Irf4 loci association in comparison to CD103+ DC (data not shown).