Mus musculus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA772806 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Gene expression in articular cartilage - subchondral bone of FRZB knockout mice
| PRJNA148643 | ENA
Project description:Purpose: RNA sequencing (RNA-Seq) analyses of articular cartilage obtained after DMM surgery in Oscar-/- and WT mice. The purpose of this experiment was to demonstrate how the deficiency of Oscar gene affects downstream signal transduction in articular cartilage. Methods: Articular cartilage mRNA profiles of 10-weeks-old wild-type (WT) and Oscar knockout (Oscar−/−) mice were performed for the destabilization of the medial meniscus (DMM) and each cartilage tissue sample was harvested from two time-points (2- and 4-weeks after surgery). Sequencing libraries were prepared according to the manufacturer’s instructions (TruSeq Stranded mRNA Library Prep Kit; Illumina, San Diego, CA, USA). Paired-end sequencing of 101-mer read length was performed using a HISEQ 2500 sequencing system (Illumina). The sequencing quality of raw FASTQ files was assessed using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Low-quality reads and adapter sequences in reads were eliminated using BBDuk (http://jgi.doe.gov/data-and-tools/bb-tools/). Results: Usinig RNA-Seq data in articular cartilage tissues from WT and Oscar–/– mice subjected to sham or DMM surgery and each cartilage sample obtained from 2- and 4-week time points after surgery, respectively. And we found that significantly enriched pathways in the 1270 common genes. Conclusions: Our study represents the Oscar gene deficiency analysis of articular cartilage transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2020-03-26 | GSE147529 | GEO
Project description:Pregnane X receptor knockout mice display aging-dependent wearing of articular cartilage
| PRJNA258189 | ENA
Project description:Using a conditional inactivation approach in the mouse, we examined the importance of SOX9 in adult growth plate and articular cartilage. We specifically investigated the roles of SOX9 in the expression of the pancartilaginous, growth-plate and articular programs and in maintaining the chondrocyte lineage fate.
2021-02-19 | GSE154381 | GEO
Project description:Using a conditional inactivation approach in the mouse, we examined the importance of SOX9 in adult growth plate and articular cartilage. We specifically investigated the roles of SOX9 in the expression of the pancartilaginous, growth-plate and articular programs and in maintaining the chondrocyte lineage fate.
2021-02-19 | GSE162033 | GEO
Project description:Osteoarthritis is a common joint disorder that causes debilitating conditions among the elderly. Risk factors of osteoarthritis include age, which is often associated with the thinning of articular cartilage. We generated conditional knockout mice that lack salt-inducible kinase 3 (Sik3) specifically in chondrocytes after birth by tamoxifen administration. Deletion of Sik3 at 2 or 8 weeks after birth increased the thickness of articular cartilage by increasing the chondrocyte population. Additionally, Sik3 deletion protected cartilage against osteoarthritis development. We identified the edible Pteridium aquilinum ingredient, pterosin B, as a compound that inhibits the Sik3 pathway. Intraarticular injection of pterosin B protected cartilage against osteoarthritis development. Sik3 deletion or pterosin B treatment inhibited activation of the hypertrophic program through the histone deacetylase 4 (Hdac4) pathway, increased Prg4 expression in chondrocytes, and protected cartilage against osteoarthritic attack. Collectively, our results suggest Sik3 is a regulator that regulates homeostasis of articular cartilage thickness and a target for treatment of osteoarthritis, and that pterosin B can be the lead compound for relevant drugs.
2016-03-21 | GSE75995 | GEO
Project description: Not available
| S-EPMC8784167 | biostudies-literature
Project description:A tissue survey of gene expression was conducted using microarray-based transcriptional profiling to compare equine articular cartilage to 10 other normal adult horse tissues. The ten comparative tissues were bladder, cerebellum, kidney, liver, lung, lymph node, muscle, placental villous, spleen, and testis. Messenger RNA transcriptome comparisons were conducted between equine articular cartilage and ten other body tissues using a 9413 element equine-specific cDNA microarray and a two-color dye-swap experimental design. After scanning, the median intensities adjusted for background were entire chip Lowess-normalized for each individual slide. Quantile regression was used to estimate the conditional quantile of the M and A log ratios given the observed average log intensity. Briefly, a nonparametric approach was used to reveal the relationship between percentiles of M and A, where M is log2 (R/G) and A is 0.5 log2 (RG) with R representing expression in articular cartilage and G representing expression in the comparative tissue. The quantile regression was fit using a B-spline with 5 fixed nodes. The 1st, 5th, 10th, 20th, 50th, 80th, 90th, 95th, and 99th conditional quantiles were estimated. For each observed gene intensity in a given tissue comparison, the normal quantile was used as the cartilage-specificity in place of the corresponding estimated regression quantile.
2011-01-27 | E-GEOD-23862 | biostudies-arrayexpress