Project description:To profile the overall transcriptomic changes, we performed RNA-seq with bone marrow macrophages (BMM) before and after osteoclast differentiation (day 0 vs day 4). To induce mature osteoclasts formation, BMM were seeded and culture with customized αMEM containing 1/50 CMG14-12 supernatant and 75 ng/ml RANKL for 4 days.
Project description:The transcription factor ETS2 was identified as a hub gene that promotes osteoclast differentiation during the progression of osteoarthritis (OA). Virtual perturbation and in vitro perturbation experiments demonstrated that knockdown of ETS2 can inhibit osteoclast differentiation. Transcriptional regulatory network analysis and combined CUT&Tag with ATAC-seq analysis results indicate that ETS2 promotes osteoclast differentiation by targeting and enhancing the expression of CEBPB.
Project description:The aim of this analysis was to investigate the changes in the gene expression pattern of ex vivo cultured wildtype murine osteoclasts during the course of osteoclastogenic differentiation.
Project description:Bisphosphonates are the mainstay of therapy worldwide for osteoporosis. They inhibit the activities of the osteoclasts, the bone resorption cells. While bisphosphonates are known to block farnesyl pyrophsophate synthase to exert their anti-resorptive action, the detailed mechanism is not well understood. Examining the change in expression profile before and after bisphosphonate treatment in the osteoclasts might shed some light on the biological pathways that are perturbed. Osteoclastic precursor cells were treated with (or without) bisphosphonates (alendronate or risedronate) during their differentiation into mature osteoclasts.
Project description:Osteoclastogenesis is induced by the stimulation of RANKL. In the early stage of osteoclast differentiation, the osteoclast progenitor cells are primed by M-CSF, following a tightly controlled genetic program where specific sets of genes are up-regulated by RANKL. Some of them, for instance, control differentiation, cell-cell fusion and bone resorption. We used microarrays to detail the global program of gene expression underlying osteoclastogenesis and identified various up-regulated genes during this process. Macrophages and osteoclasts were cultured for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of macrophages and osteoclasts in order to increase the temporal resolution of expression profiles. To that end, mouse bone marrow cells were cultured in the presence of M-CSF for three days and harvested as macrophage and oseteoclast common progenitor cells. Then common progenitor cells were further cultured in the presence of M-CSF alone for macrophages and M-CSF plus RANKL for osteoclasts, respectively.
Project description:Mouse WT129 ESCs were differentiated into glutamatergic neurons and samples were collected at days 0 (mESCs), 4 (embryoid bodies), 8 (neuronal precursors) and 12 (neurons). ATAC-seq experiment in 4 biological replicates was performed at 4 indicated above time points to profile chromatin structure changes during differentiation.
Project description:We have used ATAC-seq to track cell state changes that occur during the differentiation of mouse embryonic stem cells to defined neural progenitor fates. We have performed ATAC-seq every 24 hours in cells en route to 3 distinct neural progenitors fates, anterior, hindbrain and spinal cord. This has allowed us to define how cells transition to a neural state, based on their enhancer usage. We identified regions distinct to different anterior-posterior neural progenitors, and validated their relevance by performing in vivo ATAC-seq on neural progenitors isolated from different axial levels of mouse embryos.