GEO DataSets

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

Organism:

Homo sapiens

Type:

Expression profiling by array; Methylation profiling by array

Platforms:

GPL11532 GPL8490

64 Samples

Download data: CEL

(Submitter supplied) The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. Genome wide DNA methylation profiling of normal and osteoarthritic samples. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in cartilage knee samples. more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL8490

41 Samples

Download data: TXT

(Submitter supplied) The aim of this study is to identify, for the first time, the genome-wide DNA methylation profiles of human articular chondrocytes from OA and healtly cartilage samples. A subsequent validation of methylation profiles were performed in an idependent cohort of OA samples with Affymetrix Hugene 1.1 st array This represents the gene expression component of the study only

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL11532

23 Samples

Download data: CEL

(Submitter supplied) Genome wide gene expression was determined in paired samples of OA affected and preserved cartilage of the same joint using microarray analysis for 33 patients of the RAAK-study. Among the 1717 genes that were significantly different expressed between OA affected and preserved cartilage we found significant enrichment for genes involved in skeletal development (e.g. TNFRSF11B and FRZB). Also several inflammatory genes such as CD55, PTGES and TNFAIP6, previously identified in within-joint analyses as well as in analyses comparing preserved cartilage from OA affected joints versus healthy cartilage were among the top genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6947

73 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL6244 GPL11154

15 Samples

Download data: CEL

(Submitter supplied) Examination of the genome-wide distribution of 5hmC in osteoarthritic chondrocytes compared to normal chondrocytes in order to elucidate the effect on OA-specific gene expression. 5hmC-sequencing was performed and data was compared with microarray gene expression data to identify genes with differential expression between normal and OA chondrocytes that are potentially under epigenetic regulation.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

7 Samples

Download data: CEL

(Submitter supplied) Examination of the genome-wide distribution of 5hmC in osteoarthritic chondrocytes compared to normal chondrocytes in order to elucidate the effect on OA-specific gene expression. 5hmC-sequencing was performed and data was compared with microarray gene expression data to identify genes with differential expression between normal and OA chondrocytes that are potentially under epigenetic regulation.

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL11154

8 Samples

Download data: TXT

(Submitter supplied) Cartilage samples were collected from hip or knee joint replacement patients either due to primary OA or hip fractures as controls. DNA was extracted from the collected cartilage and assayed by Illumina Infinium HumanMethylation450 ‎BeadChip array, which allows for the analysis of >480,000 CpG sites.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

18 Samples

Download data: IDAT, TXT

(Submitter supplied) The aim of this study was to characterise the genome-wide DNA methylation profile of osteoathritis (OA) chondrocytes from both knee and hip cartilage, providing the first comparison of DNA methylation between OA and non-OA hip cartilage, and between OA hip and OA knee cartilage. The study was performed using the Illumina Infinium HumanMethylation450 BeadChip array. Genome-wide methylation was assesed in chondrocyte DNA extracted from 23 OA hip, 73 OA knee and 21 healthy hip controls (NOF - neck of femure samples). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

97 Samples

Download data: IDAT, 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) The aim of this study was to identify DNA methylation patterns in femur trabecular bone and cartilage of age-matched female baboons, five with and five without knee osteoarthritis. The Illumina Infinium Human Methylation450 BeadChip was used to assess these genome-wide methylation patterns.

Organism:

Homo sapiens; Papio sp.

Type:

Methylation profiling by genome tiling array

Platform:

GPL16304

20 Samples

Download data: CSV, IDAT

(Submitter supplied) The aim of the current study was to identify molecular markers for articular cartilage that can be used for the quality control of tissue engineered cartilage. Therefore a genom-wide expression analysis was performed using RNA isolated from articular and growth plate cartilage, both extracted from the knee joints of minipigs. Keywords: Native material or primary cells isolated from articular cartilage and growth plate cartilage

Organism:

Sus scrofa

Type:

Expression profiling by array

Platform:

GPL3533

6 Samples

Download data: CEL, CHP

(Submitter supplied) The recruitment of mesenchymal stem cells in order to reconstruct damaged cartilage of osteoarthritis joints is a challenging tissue engineering task. Vision towards this goal is blurred by a lack of knowledge about the underlying differences between chondrocytes and MSC during the chondrogenic cultivation process. The aim of this study was to shed light on the differences between chondrocytes and MSC occurring during chondral differentiation through tissue engineering. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Dataset:

GDS3785

Platform:

GPL9828

8 Samples

Download data: CEL

Temporal analysis of chondrocytes from osteoarthritic knee joints and mesenchymal stem cells from bone marrow of healthy donors, grown in a pellet culture system under chondrogenic conditions. Results provide insight into molecular mechanisms underlying chondrogenic commitment of both cell types.

Organism:

Homo sapiens

Type:

Expression profiling by array, transformed count, 2 cell type, 4 time sets

Platform:

GPL9828

Series:

GSE19664

8 Samples

Download data: CEL

(Submitter supplied) Single-cell transcriptomics analysis of human knee articular cartilage tissue to present a comprehensive transcriptome atlas and osteoarthritis-critical cell populations.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

19 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) The characterization of knee articular cartilage changes with different zones -- articular surface, (AS), superficial zone (SZ), middle zone (MZ), and deep zone (DZ) -- based on the organization of the tissue and the alignment degree of collagen fibers. To comprehensively explore the spatial landscape of chondrocytes on human knee articular cartilage, we carried out the laser capture microdissection (LCM) coupled with full-length mRNA sequencing.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

124 Samples

Download data: CSV

(Submitter supplied) We report an immortalised CRISPR-Cas9 mesenchymal stem cell line knockdown of Plectin, we initally noted that patients with osteoarthritis association single nucelotide polymorphism rs11780978 had a correlation between genotype at rs11780978 and allelic expression imbalance, with a reduced expression of Plectin from the risk allele. We replicated the effect of the risk allele by deleting 26bp from exon 3 of Plectin to generate multiple knockdown lines to assess the molecular phenotype of Plectin knockdown in the cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: TXT

(Submitter supplied) We employed Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) to map the accessible chromatin landscape in articular knee cartilage of OA patients. We identified 109,215 accessible chromatin regions for cartilages, of which 71% were annotated as enhancers. By overlaying them with genetic and DNA methylation data, we have determined potential OA-relevant enhancers and their putative target genes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL11154

16 Samples

Download data: BIGWIG

(Submitter supplied) Understanding the molecular mechanisms underlying human cartilage degeneration and regeneration is helpful for improving therapeutic strategies for treating osteoarthritis (OA). Here, we report the molecular programmes and lineage progression patterns controlling human OA pathogenesis using single-cell RNA sequencing (scRNA-seq). We performed unbiased transcriptome-wide scRNA-seq analysis, computational analysis and histological assays on 1464 chondrocytes from 10 patients with OA undergoing knee arthroplasty surgery. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

34 Samples

Download data: TXT, XLSX