Genome-wide maps of chromatin state and RNA-seq in WT and Dnmt3a KO BMDMs (bone marrow derived macrophages) [RRBS, ATAC-seq, CHIP-seq]

To identify soluble factors released from Dnmt3a KO macrophages that might drive differences in osteoclast differentiation, we performed RNA sequencing on unstimulated BMDMs from WT and Dnmt3a KO mice. To investigate the mechanistic basis for the inflammatory phenotype. of myeloid cells with loss of Dnmt3a,we performed reduced representation bisulfite sequencing (RRBS) on Dnmt3a KO and WT BMDMs to assess methylation changes. Concurrently, we performed ATAC-sequencing (ATAC-seq) to assess differences in chromatin accessibility between WT and Dnmt3a KO BMDMs in the context of changes in methylation. We performed chromatin immunoprecipitation sequencing (CHIP-seq) for Irf3 and Rela based on ATAC-seq analysis. RRBS, ATAC-seq, CHIP-seq in WT and Dnmt3a KO BMDMs on day 8-10 of differentiation with or without LPS (10ng/ml for 6 hours for chromatin-related sequencing.