GEO DataSets

(Submitter supplied) Purpose: Osteoblast cells mature from a mesenchymal stem cell pool to become cells capable of forming bone matrix and mineralizing this matrix. The goal of this study was to characterize temporal changes in the transcriptome across osteoblast maturation, starting with committed mesenchymal stem cell/ early pre-osteoblast stage through to mature osteoblasts capable of matrix mineralization. Methods: Enriched populations of pre-osteoblast like cells were obtained from neonatal calvaria from C57BL/6J mice expressing CFP under the control of the Col3.6 promoter. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

27 Samples

Download data: TXT

(Submitter supplied) In our study, we leveraged RNA-seq data from four different human osteoblast cell lines and ATAC-seq data from one human osteoblast cell line to identify target genes for plausibly causal SNPs influencing bone density. We also re-called ENCODE generated osteoblast DNase hypersensitive sites, and have uploaded them here for sharing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

5 Samples

Download data: BEDGRAPH, TXT

(Submitter supplied) Bone mineral density (BMD) is a strong predictor of osteoporotic fracture. It is also one of the most heritable disease-associated quantitative traits. As a result, there has been considerable effort focused on dissecting its genetic basis. Here, we performed a genome-wide association study (GWAS) in a panel of inbred strains to identify associations influencing BMD. This analysis identified a significant (P=3.1 x 10-12) BMD locus on Chromosome 3@52.5 Mbp that replicated in two seperate inbred strain panels and overlapped a BMD quantitative trait locus (QTL) previously identified in a F2 intercross. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TAB

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Download data

(Submitter supplied) The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Download data: XLSX

(Submitter supplied) The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Download data: XLSX

(Submitter supplied) The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Download data: XLSX

(Submitter supplied) The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Download data: XLSX

(Submitter supplied) The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored the International Mouse Phenotyping Consortium (IMPC) for the analysis of skeletal data from 3,974 mutant strains for bone mineral density (BMD), a measure that is frequently altered in a range of bone pathologies including osteoporosis. A total of 200 genes were found to significantly affect BMD. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Third-party reanalysis

Download data: XLSX

(Submitter supplied) Significant advances have been made in the discovery of genes affecting bone mineral density (BMD); however, our understanding of its genetic basis remains incomplete. In the current study, genome-wide association (GWA) and co-expression network analysis was used in the recently described Hybrid Mouse Diversity Panel (HMDP) to identify and functionally characterize novel BMD genes. In the HMDP, a GWA of total body, spinal and femoral BMD revealed four significant associations (-log10P > 5.39) affecting at least one BMD trait on chromosomes (Chrs.) 7, 11, 12 and 17. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6105

149 Samples

Download data: TXT

(Submitter supplied) The common genetic variants associated with complex traits typically lie in non-coding DNA and may alter gene regulation in a cell-type specific manner. Consequently, the choice of tissue or cell model in the dissection of disease associations is important. We carried out an eQTL study of primary human osteoblasts (HOb) derived from unrelated donors of Swedish origin, each represented by two independently derived primary lines to provide biological replication. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6104

187 Samples

Download data: TXT

(Submitter supplied) Genome-wide association studies (GWASs) for bone mineral density (BMD), one of the most significant predictors of osteoporotic fracture, have identified over 1100 independent associations; however, few of the causal genes have been identified. Recently, the “omnigenic” model of the genetic architecture of complex traits proposed two general categories of causal genes, core and peripheral. Core genes play a direct role in regulating traits; thus, their identification is key to revealing critical regulators and potential therapeutic targets. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

96 Samples

Download data: CSV

(Submitter supplied) Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene identification and a strict focus on bone mineral density (BMD). Here, we used Diversity Outbred (DO) mice to directly address these limitations by performing the first systems genetics analysis of over 50 complex skeletal phenotypes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

1 Sample

Download data: MTX, TSV

(Submitter supplied) Genome-wide association studies (GWASs) for osteoporotic traits have identified over 1000 associations; however, their impact has been limited by the difficulties of causal gene identification and a strict focus on bone mineral density (BMD). Here, we used Diversity Outbred (DO) mice to directly address these limitations by performing the first systems genetics analysis of over 50 complex skeletal phenotypes. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

192 Samples

Download data: CSV

(Submitter supplied) We recently identified Bicc1 as a regulator of osteoblast differentiation and bone mass. Bicc1 encodes an RNA-binding protein. Here, we have used siRNA to decrease Bicc1 expression in primary calvarial osteoblasts. Illlumina microarrays were then used to profile global gene expression changes.

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS5249

Platform:

GPL6885

16 Samples

Download data: TXT

Analysis of calvarial osteoblasts transfected with siRNAs targeting bicaudal C homolog 1 (constructs BICC1_1, BICC1_2 and BICC1_3). Bicc1 encodes an RNA-binding protein. Results provide insight into the role of Bicc in osteoblastogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 4 protocol sets

Platform:

GPL6885

Series:

GSE51693

16 Samples

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