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Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [HsMmMicroarray]

ABSTRACT: Similar temporal expression kinetics of transcription factors in human and mouse osteoclast differentiation evaluated by microarray We used the identical differentiation conditions to evaluate gene expression kinetics of mouse and human osteoclast differentiation by microarray

OTHER RELATED OMICS DATASETS IN: PRJNA419649PRJNA419645PRJNA419647PRJNA419648

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE107295 | GEO | 2018/04/10

REPOSITORIES: GEO

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Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

Project description:Eavluation of temporal expression kinetics during mouse osteoclast differentiation evaluated by microarray. We overlayed gene expression data with correspoding DNA binding data from MITF and PU.1 ChIP-seq to evaluate gene regulatory networks in osteoclasts.

2018-04-10 | GSE107296 | GEO

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

Project description:Genome-wide association studies (GWASs) have been instrumental in understanding complex phenotypic traits. However, they have rarely been used to understand lineage-specific pathways and functions that contribute to the trait. In this study, by integrating publicly available lineage-specific enhancers from mesenchymal and myeloid compartments with bone mineral density loci, we were able to segregate osteoblast- and osteoclast (OC)-specific functions. Specifically, in OCs, a PU.1-dependent transcription factor (TF) network was revealed. Further we conducted functional genomic analysis PU.1 and MITF genome wide binding with corresponding gene expression analysis which revealed a TF network essential for OC differentiation. Several of these TFs were regulated by cooperative binding of PU.1 with BRD4 to form superenhancers. Further, PU.1 is essential for conformational changes in the superenhancer region of Nfatc1. In summary, our study demonstrates that utilizing GWASs with genome-wide binding studies as a filter helps to decipher lineage-specific pathways contributing to complex disease states.

2018-04-10 | GSE107294 | GEO

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-04-10 | GSE107297 | GEO

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts

| PRJNA419645 | ENA

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [HsMmMicroarray]

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [HsMmMicroarray]

| PRJNA419647 | ENA

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [ChIP-seq]

| PRJNA419648 | ENA

Expression data from cultured macrophages and osteoclasts

2010-03-22 | GSE20850 | GEO

Expression data from cultured macrophages and 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.

2010-03-22 | E-GEOD-20850 | biostudies-arrayexpress

Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

Project description:Bone density loci identified by genome-wide association studies segregate a lineage-specific PU.1-dependent gene regulatory network in osteoclasts [MoEx-1_0-st array]

| PRJNA419649 | ENA

Comprehensive transcriptome analysis of osteoclasts with the SIK3 deletion and pterosin B treatment.

Project description:Maintenance of bone homeostasis and the balance between bone resorption and formation are crucial for maintaining skeletal integrity. Osteoclasts are responsible for bone resorption and play a vital role in this process. The role of salt-inducible kinase 3 (SIK3) in osteoclast differentiation and maturation and its potential as a therapeutic target for osteoporosis remain poorly understood. Here, we generated osteoclast-specific Sik3 conditional knockout (cKO) mice and investigated the effects of SIK3 deletion on bone homeostasis. Our findings revealed increased bone mineral density and an osteopetrosis phenotype in Sik3 cKO mice, indicating the involvement of SIK3 in bone resorption. Furthermore, we examined the effect of pterosin B, an SIK3 inhibitor, on osteoclast differentiation. Pterosin B treatment inhibits osteoclast differentiation in vitro, reduces the number of multinucleated osteoclasts, and suppresses bone resorption. Therefore, in this study, to better understand the molecular mechanism of SIK3 in osteoclast differentiation and maturation, we performed gene expression profiling of bone marrow monocytes from SIK3 deletion and pterosin B treated mice using RNA sequencing (RNA-seq).

2024-07-21 | GSE234221 | GEO

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