Single Cell Cortical Bone Transcriptomics from Sost-Cre
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA858479 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20168822.fastq.gz | Fastqsanger.gz | |||
| SRR20168823.fastq.gz | Fastqsanger.gz |
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Project description:Single cell cortical bone transcriptomics from Sost-Cre enriched cell population.
2023-01-24 | GSE208152 | GEO
Project description:Purpose: The purpose of this study is to identify the age when the skeletal muscle phenotype in Sost-CreERT2 mice occurs. Methods: Gastrocnemius skeletal muscle mRNA profiles of 1-month-old Sost-CreERT2 and wild type Cre- male mice and 3-month-old Sost-CreERT2 and wild type Cre- female mice were generated by deep sequencing, in triplicate, using HiSeq4000. The sequencing data were first assessed using FastQC (Babraham Bioinformatics, Cambridge, UK) for quality control. Then all sequenced libraries were mapped to the mm10 mouse genome using STAR RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”. The reads distribution across the genome was assessed using bamutils (from ngsutils). Uniquely mapped sequencing reads were assigned to mm10 refSeq genes using featureCounts (from subread) with the following parameters: “-s 2 -p –Q 10”. Quality control of sequencing and mapping results was summarized using MultiQC. Genes with read count per million (CPM) > 0.5 in more than 2 of the samples were kept. The data was normalized using TMM (trimmed mean of M values) method. Differential expression analysis was performed using edgeR. False discovery rate (FDR) was computed from p-values using the Benjamini-Hochberg procedure. Results: In the male mice there were 1,857 2fold upregulated genes and 1,959 2fold downregulated genes, whereas in females there were 37 upregulated and 34 downregulated genes. Only 14 upregulated and 21 downregulated genes overlapped between males and females. A pathway analysis of the male gastrocnemius was performed showing that inflammation mediated by chemokine and cytokine signaling pathways was the major upregulated pathway in Sost-CreERT2 as compared to wild type Cre– male mice. The Wnt signaling pathway was the major downregulated pathway in the Sost-CreERT2 male mice.
2018-11-29 | GSE119761 | GEO
Project description:A haplotype block at the sclerostin (SOST) gene correlates with bone mineral density (BMD) and increased periodontitis risk in smokers. Investigating the putative causal variants within this block, our study aimed to elucidate the impact of linked enhancer elements on gene expression and to evaluate their role on transcription factor (TF) binding. Using CRISPR/dCas9 activation (CRISPRa) screening in SaOS-2 cells, we quantified disease-related enhancer activities regulating SOST expression. Additionally, in SaOs2-cells, we investigated the influence of the candidate TFs CCAAT/enhancer-binding protein beta (CEBPB) on gene expression by antisense (GapmeR) knockdown, followed by RNA sequencing. The periodontitis-linked SNP rs9783823 displayed a significant cis-activating effect (25-fold change in SOST expression), with the C-allele containing a CEBPB binding motif (position weight matrix (PWM) = 0.98, Pcorrected = 7.7 x 10-7). CEBPB knockdown induced genome-wide upregulation but decreased epithelial-mesenchymal transition genes (P= 0.71, AUC = 2.2 x 10-11). This study identifies a robust SOST cis-activating element linked to BMD and periodontitis, carrying CEBPB binding sites and highlights CEBPB's impact on epithelial-mesenchymal transition.
2024-06-27 | GSE269019 | GEO
Project description:Comparison Between Sost-CreERT2 and wild type Cre- Gastrocnemius Skeletal Muscle Transcriptomes
| PRJNA490193 | ENA
Project description:WNT signaling is critical in most aspects of skeletal development and homeostasis, and antagonists of WNT signaling are emergning as key regulatory proteins with great promise as therapeutic agents for bone disorders. Until recently Sost and its paralog Sostdc1 have been described as growth factors with highly restricted expression in the adult where Sost was assumed 'osteocyte-' and Sostdc1 'kidney-' specific. Here we show that these two proteins emerged throgh ancestral genome duplication and their expression patterns have diverged to span complimentary domains in most organ systems including musculoskeletal, cardiovascular, nervous, digestive, reproductive and respiratory. In the developing limb, Sost and Sostdc1 display dynamic expression patterns with Sost being restricted to the distal ectoderm and Sostdc1 to the proximal ectoderm and the mesenchyme. While Sostdc1-/- mice lack any obvious limb and skeletal defects, Sost-/- mice recapitulate the hand defects described for sclerosteosis patients. However, elevated WNT signaling in Sost-/-; Sostdc1-/- mice causes misregulation of SHH signaling, ectopic activation of Sox9 in the digit 1 field and ultimately preaxial polydactyly. In addition, we show that the syndactyly documented in Sclerosteosis is present in both Sost-/- and Sost-/-; Sostdc1-/- mice, and is driven by misregulation of Fgf8 in the AER, a region lacking Sost and Sostdc1 expression. This study highlights the complexity of WNT signaling in skeletal biology and disease and emphasizes how redundant mechanisms and non-cell autonomous effects can synergize to unveil new intricate phenotypes caused by elevated WNT signaling. Five arrays were analyzed, consisting of two total embryonic fore-limb RNA (experimental) and three total embryonic forelimb RNA (reference) samples at E11.5 DPC mouse (C57Bl6 strain). Embryos were not pooled to generate samples. Each time point has 3 to 5 biological replicates for limb bud samples, duplicates for whole embryos. Comparisons were made between limb bud samples and whole embryo at the same stage, fore-limb samples of different stages, hind-limb samples of different stages, and fore-limb samples compared to hind-limb samples at the same or the next stage.
2013-08-17 | E-GEOD-44325 | biostudies-arrayexpress
Project description:Here we provide proteomic datasets of pairs of cortical and trabecular bone from six Early Holocene Caprinae rib fragments from the site of La Draga, Spain, using shotgun proteomics. Our observations on proteome size and protein, peptide, and amino acid degradation have implications for the sampling of archaeological skeletal remains in highly degraded proteomic contexts, where preference should be given to the sampling of cortical bone in order to maximise the retrieval of larger and better-preserved skeletal proteomes.
2024-07-12 | PXD047126 | Pride
Project description:WNT signaling is critical in most aspects of skeletal development and homeostasis, and antagonists of WNT signaling are emergning as key regulatory proteins with great promise as therapeutic agents for bone disorders. Until recently Sost and its paralog Sostdc1 have been described as growth factors with highly restricted expression in the adult where Sost was assumed 'osteocyte-' and Sostdc1 'kidney-' specific. Here we show that these two proteins emerged throgh ancestral genome duplication and their expression patterns have diverged to span complimentary domains in most organ systems including musculoskeletal, cardiovascular, nervous, digestive, reproductive and respiratory. In the developing limb, Sost and Sostdc1 display dynamic expression patterns with Sost being restricted to the distal ectoderm and Sostdc1 to the proximal ectoderm and the mesenchyme. While Sostdc1-/- mice lack any obvious limb and skeletal defects, Sost-/- mice recapitulate the hand defects described for sclerosteosis patients. However, elevated WNT signaling in Sost-/-; Sostdc1-/- mice causes misregulation of SHH signaling, ectopic activation of Sox9 in the digit 1 field and ultimately preaxial polydactyly. In addition, we show that the syndactyly documented in Sclerosteosis is present in both Sost-/- and Sost-/-; Sostdc1-/- mice, and is driven by misregulation of Fgf8 in the AER, a region lacking Sost and Sostdc1 expression. This study highlights the complexity of WNT signaling in skeletal biology and disease and emphasizes how redundant mechanisms and non-cell autonomous effects can synergize to unveil new intricate phenotypes caused by elevated WNT signaling.
2013-08-17 | GSE44325 | GEO
Project description:Er:YAG laser irradiation decreases Sost expressions in bone and osteogenic cell
| PRJNA609661 | ENA
Project description:The goal of this study was to perform RNA-sequencing of cortical bone isolated from 11-week-old female hindlimb unloaded and control mice. Mice were subjected to hindlimb unloading for 7 days, followed by RNA isolation of cortical bone. Cortical transcriptomic profiles were assessed with RNAseq.
2021-03-23 | GSE169292 | GEO
Project description:Large-scale transcriptional profiling has enormous potential for discovery of osteoporosis susceptibility genes and for identification of the molecular mechanisms by which these genes and associated pathways regulate bone maintenance and turnover. A potential challenge in the use of this method for the discovery of osteoporosis genes is the difficulty of obtaining bone tissue samples from large numbers of individuals. In this study, we tested the applicability of using peripheral blood mononuclear cell (PBMC)-derived transcriptional profiles as a surrogate to cortical bone transcriptional profiles to address questions of skeletal genetics. We used a well-established and genetically well-characterized nonhuman primate model for human bone maintenance and turnover. We determined that a high degree of overlap exists in gene expression of cortical bone and PBMCs and that genes in both the osteoporosis-associated RANK Osteoclast and Estrogen Receptor Signaling pathways are highly expressed in PBMCs. Genes within the Wnt Signaling pathway, also implicated in osteoporosis pathobiology, are expressed in PBMCs, albeit to a lesser extent. These results are the first in an effort to comprehensively characterize the relationship between the PBMC transcriptome and bone M-bM-^@M-^S knowledge that is essential for maximizing the use of PBMCs to identify genes and signaling pathways relevant to osteoporosis pathogenesis. It is also a first step in identifying genes that correlate in a predictable manner between PBMCs and cortical bone from healthy and osteoporotic individuals, potentially allowing us to identify genes that could be used to diagnose osteoporosis prior to detectible bone loss and with easily obtained PBMCs. Total RNA was isolated from peripheral blood mononuclear cells and cortical bone of a nonhuman primate model (Papio hamadryas ssp.) of bone maintenance and turnover. Both samples were taken from the same animal. Tissue from 15 animals was used for the study.
2013-10-22 | E-GEOD-51495 | biostudies-arrayexpress