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Links from GEO DataSets

Items: 15

1.

Single-cell RNA-seq of bone marrow-derived stromal cells from 5 Diversity Outbred mice

(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
Series
Accession:
GSE152806
ID:
200152806
2.

Systems genetic analysis in Diversity Outbred mice informs human bone mineral density GWAS and identifies Qsox1 as a novel determinant of bone strength

(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
Series
Accession:
GSE152708
ID:
200152708
3.

Mouse Genome-Wide Association and Systems Genetics Identifies Lipoma HMGIC Fusion Partner (Lhfp) as a Regulator of Bone Mass

(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
Series
Accession:
GSE121887
ID:
200121887
4.

Transcriptomic Profiling of Primary Osteoblast from a panel of Collaborative Cross mice

(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
Series
Accession:
GSE134081
ID:
200134081
5.

Bone microarray profiles from the Hybrid Mouse Diversity Panel

(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
Series
Accession:
GSE27483
ID:
200027483
6.

Osteoblast Gene Expression in Response to Bicc1 Knockdown

(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
Series
Accession:
GSE51693
ID:
200051693
7.
Full record GDS5249

Bicaudal C homolog 1 knock down effect in primary calvarial osteoblasts

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
Download data
8.

Temporal gene expression across osteoblastogenesis.

(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
Series
Accession:
GSE54461
ID:
200054461
9.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus
Type:
Expression profiling by array; Third-party reanalysis
Download data
Series
Accession:
GSE158151
ID:
200158151
10.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoclast_0_3days]

(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
Series
Accession:
GSE158150
ID:
200158150
11.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoclast_48H_samples]

(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
Series
Accession:
GSE158149
ID:
200158149
12.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Osteoblast_5days]

(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
Series
Accession:
GSE158148
ID:
200158148
13.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Unsorted_Osteoblast_7_17days]

(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
Series
Accession:
GSE158147
ID:
200158147
14.

Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density [Sorted_Osteoblast_7_17days]

(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
Series
Accession:
GSE158146
ID:
200158146
15.

An atlas of genetic influences on osteoporosis in humans and mice

(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
Series
Accession:
GSE120755
ID:
200120755
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