GEO DataSets

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by array

Platforms:

GPL21103 GPL21827

18 Samples

Download data: TXT

(Submitter supplied) Using large-scale patient data sets and genetically engineered (inducible conditional knockout and knockin) mouse models, we show that a novel transcript of long noncoding RNA ELDR is essential for the development of chondrocyte senescence.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: XLSX

(Submitter supplied) Using large-scale patient data sets and genetically engineered (inducible conditional knockout and knockin) mouse models, we show that a novel transcript of long noncoding RNA ELDR is essential for the development of chondrocyte senescence.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

6 Samples

Download data: XLSX

(Submitter supplied) To investigate lncRNA profile in OA patients and analyze the critical role of lncRNA in chondrocyte senescence To investigate lncRNA profile in OA patients and analyze the critical role of lncRNA in chondrocyte senescence

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL21827

6 Samples

Download data: TXT

(Submitter supplied) Purpose: The aims of this study were to identify differentially expressed genes between Kdm6bf/f and Col2a1-CreERT2;Kdm6bf/f primary chondrocytes. Methods: RNA samples of primary chondrocytes were prepared from Kdm6bf/f and Col2a1-CreERT2;Kdm6bf/f mice and were sequenced and analyzed by Shanghai Novel Bioinformatics Co, Ltd. Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences, reads with >5% ambiguous bases (noted as N) and low-quality reads containing more than 20 percent of bases with qualities of <13. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18635

3 Samples

Download data: TXT

(Submitter supplied) Using RNA sequencing (Illumina Hi-Seq 2000 sequencer) we report the transcriptome profile of primary human chondrocytes isolated from patients with hip osteoarthritis (OA), and the transcriptome response of these cells to 4h stimulation with IL-1β (1ng/ml). In total, 983 long non-coding RNAs (lncRNAs) were identified, which included 642 intergenic lncRNAs (lincRNAs), 124 antisense and pseudogenes. Less than 4% of the identified lncRNAs overlapped with putative eRNAs regions, and visual inspection showed that they were uni-directional and multi-exonic. Upon IL-1β stimulation 499 protein-coding genes were differentially expressed, and 158 lncRNAs were differentially expressed, including 92 lincRNAs, 13 antisense and 18 psudogenes. This study demonstrates that IL-1β induces a rapid and widespread change in the transcriptome of the primary human OA chondrocyte.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT

(Submitter supplied) Osteoarthritis (OA) is a common degenerative disease of the joint. Data from our lab indicates that Hedgehog (Hh) signaling is activated in human OA and murine models of OA (Lin et al., 2009, Nature Medicine). To identify Hh target genes, microarray analyses were performed to detect changes in gene expression when the Hh pathway was inhibited in human OA cartilage samples. Identifying Hh target genes in chondrocytes will elucidate key regulatory networks that govern chondrocyte homeostasis and provide novel therapeutic strategies for OA.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

6 Samples

Download data: CEL, CHP

(Submitter supplied) Gene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expressing the zinc transporter ZIP8 (SLC39A8) protein. In this study, we have attempted to explore the effects of ZIP8 overexpression on mouse transcriptome and have identified numerous genes which are involved in osteoarthritis pathogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

8 Samples

Download data: CEL

(Submitter supplied) mRNA profiles of primary mouse chondrocytes transfected with miR-Ctrl or miR-204 mimics were generated by mRNA sequencing. This study provides insights into the role of miR-204 in chondrocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) miRNA profiles of primary mouse chondrocytes exposed to prolonged normoxia, which resulted in accumulation of oxidative stress. The sequencing data were generated by miRNA sequencing, in three biological replicates. This study provides insights into the role of chronic oxidative stress in chondrocytes and helps identification of miRNAs related to OA pathogenesis.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL17021

6 Samples

Download data: TSV

(Submitter supplied) To investigate the function of Myl3 in in primary chondrocytes, we generated Col2a1-Cre: Myl3fl/fl (Myl3-KO) conditional knockout mice.We then performed RNA sequencing analysis with primary chondrocytes from Myl3-KO or control mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

2 Samples

Download data: XLS

(Submitter supplied) To investigate the alterations in the transcriptome profile due to adseverin deletion in articular chondrocytes, differential gene expression profiling analysis was performed using data obtained from RNA sequencing of articular chondrocytes in the native cartilage of 10 week old mice

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: TXT

(Submitter supplied) Hyaloid cartilage fibrosis is one of the important reasons for the poor prognosis of advanced osteoarthritis (OA), and is the main factor leading to joint stiffness and deformity. However, the mechanism of hyaline cartilage fibrosis remains largely unclear. Here we report that DDX5, one of the founding members of the DEAD-box RNA helicase family, was dramatically down-regulated in the degenerated articular cartilage of aged mice, and patients with OA, mouse destabilization of the medial meniscus (DMM) models，and cytokine (Interleukin (IL)-1β and tumor necrosis factor (TNF)-α) stimulation.In vitro and in vivo experimental findings that inhibition of DDX5 expression increases the fibrocartilage phenotype by reduction collagen type I (COL I) protein expression and up-regulate collagen type II (COL II) protein expression. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

12 Samples

Download data: TXT

(Submitter supplied) Genome-wide association studies (GWAS) have identified over 100 loci associated with OA risk, but the majority of OA risk variants are non-coding, making it difficult to identify the impacted genes for further study and therapeutic development. To address this need, we used a multi-omic approach and genome editing to identify and functionally characterize putative OA risk genes. Computational analysis of GWAS and ChIP-seq data revealed that chondrocyte regulatory loci are enriched for OA risk variants. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

8 Samples

Download data: BEDPE, BW, HIC, NARROWPEAK