GEO DataSets

(Submitter supplied) ChIP-seq with anti-HA tag antibody in TC28a2 cells transfected with HA-KLF4.We performed genome-wide analysis for KLF4-DNA association in TC28a2 human chondrocyte cells, to elucidate regulatory mechanisms of chondrogenic genes by KLF4.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) We performed global gene expression analysis in mocetinostat- and DMSO-treated TC28a2 human chondrocyte cells, to study genes regulated by mocesinostat comprehensively.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

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

Platform:

GPL30173

48 Samples

Download data: BIGWIG, NARROWPEAK

(Submitter supplied) We performed global gene expression analysis in Ad-KLF4-, Ad-EGFP- and non-transduced TC28a2 human chondrocyte cells, to study genes regulated by KLF4 comprehensively.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

42 Samples

Download data: CSV, XLSX

(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) Gene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expressing the hypoxia inducible factor-2 alpha (HIF-2α) protein. In this study, we have attempted to explore the effects of HIF-2α 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) Gene expression profiling of primary mouse articular chondrocyte treated with interleukin-1β. In this study, we have attempted to explore the effects of interleukin-1β on mouse transcriptome and have identified numerous genes which are involved in osteoarthritis pathogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

6 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL18573 GPL30173

38 Samples

Download data: MTX, TSV

(Submitter supplied) Osteoarthritis (OA) affects all tissues in the knee joint but therapeutic targets have often been selected for their role in cartilage damage and inflammation and largely omitted consideration of mechanisms that are mediating meniscus damage and more importantly there have been insufficient efforts to determine whether pathogenic processes are shared between tissues. Several scRNA-seq analyses have been performed in OA knees but have been largely restricted to the analysis of a single joint tissue of articular cartilage, or meniscus with the exception of one study that analyzed cartilage and synovium. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

26 Samples

Download data: MTX, TSV

(Submitter supplied) To investigate the role of ZEB1 in chondrocytes, we transfected an overexpression vector containing cDNA for ZEB1 (Sino Biological; HG17705-UT) into TC28a2 cells using Lipofectamine 3000. We then performed DRUG-seq analysis to determine the impact of ZEB1 on global gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

(Submitter supplied) To investigate the role of FAP in chondrocytes, we transfected an overexpression vector containing cDNA for FAP (Sino Biological; HG10464-UT) into TC28a2 cells using Lipofectamine 3000. We then performed DRUG-seq analysis to determine the impact of FAP on global gene expression.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30173

6 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

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

Platform:

GPL21103

45 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) We report bulk RNA-sequencing, ChIP-seq, and ATAC-seq of endothelial cells harvested from heart and lung of multiple mouse strains investigating the role of KLF2 and KLF4 in endothelial transcription

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TSV

(Submitter supplied) We report bulk RNA-sequencing, ChIP-seq, and ATAC-seq of endothelial cells harvested from heart and lung of multiple mouse strains investigating the role of KLF2 and KLF4 in endothelial transcription

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

29 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) We report bulk RNA-sequencing, ChIP-seq, and ATAC-seq of endothelial cells harvested from heart and lung of multiple mouse strains investigating the role of KLF2 and KLF4 in endothelial transcription

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Gene expression profiling of primary mouse articular chondrocyte infected with recombinant adenovirus expression mouse Regnase-1 or recombinant adenovirus expressing mouse small hairpin RNA of Regnase-1. In this study, we have attempted to explore the effects of Regnase-1 overexpression or knockdown on mouse transcriptome and have identified numerous genes which are involved in osteoarthritis pathogenesis.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL16570

9 Samples

Download data: CEL

(Submitter supplied) The goal of this study was to determine the role of miR-34a in regulating chondrocyte transcript profiles. Next Generation Sequencing of total RNA extracted from mouse KO and WT chondrocytes revealed 175 significantly differentially expressed genes (84 up, 91 down) in miR-34a KO chondrocytes compared to WT cells. We are currently validating potential direct targets of miR-34a from our NGS data and performing computational pathway analysis to identify novel pathways regulated by miR-34a.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

6 Samples

Download data: TSV

(Submitter supplied) Objective:Osteoarthritis (OA) is the most prevalent joint disease. As disease-modifying therapies are not available, novel therapeutic targets need to be discovered and prioritized for their importance in mediating the abnormal phenotype of cells in OA-affected joints. Here, we generated a genome-wide molecular profile of OA to elucidate regulatory mechanisms of OA pathogenesis and to identify possible therapeutic targets using integrative analysis of mRNA-sequencing data obtained from human knee cartilage. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL18573

38 Samples

Download data: TXT, XLSX

(Submitter supplied) Cartilage mineralization is a tightly controlled process, imperative for skeletal growth and fracture repair. However, in osteoarthritis (OA), cartilage mineralization may impact the joint range of motion, inflict pain and may increase chances for joint effusion. Here we attempt to understand the link between inflammation and cartilage mineralization by targeting SIRT1 and LEF1, both reported to have contrasting effects on cartilage.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

8 Samples

Download data: TXT

(Submitter supplied) The connection between different tissues is vital for the development and function of all organs and systems. In the musculoskeletal system, the attachment of elastic tendons to stiff bones poses a mechanical challenge that is solved by the formation of a transitional tissue, which allows the transfer of muscle forces to the skeleton without tearing. Here, we show that tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, which is regulated by sharing regulatory elements with these cells and by Krüppel-like factors transcription factors (KLF). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24247

1 Sample

Download data: MTX, TSV, XLSX