Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA281618 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Osteoarthritis (OA) of the hand is a common disease resulting in pain and impaired function. The pathogenesis of hand OA (HOA) is elusive and models to study it have not been described so far. Culture of chondrocytes is a model to study the development of cartilage degeneration, which is a hallmark of OA and well established in OA of the knee and hip. In the current study we investigated the feasibility human chondrocyte culture derived from proximal interphalangeal (PIP) finger joints of dissecting room cadavers. Index and middle fingers without signs of osteoarthritis were obtained from 30 cadavers using two different protocols. Hyaline cartilage from both articulating surfaces of the proximal interphalangeal (PIP) joint was harvested and digested in collagenase. Cultured chondrocytes were monitored for contamination, viability, and expression of chondrocyte specific genes. Chondrocytes derived from knee joints of the cadavers were cultured under identical conditions. Gene expression comparing chondrocytes from PIP and knee joints was carried out using Affymetrix GeneChip Human 2.0 ST arrays. The resulting differentially expressed genes were validated by real-time PCR and immunohistochemistry.Chondrocytes harvested up to 101 hours after death of the donors were viable. mRNA expression of collagen 2A1, aggrecan and Sox9 was significantly higher in chondrocytes as compared to cultured fibroblasts. Comparison of gene expression by chondrocytes from PIP and knee joints yielded 528 differentially expressed genes. Chondrocytes from the same joint region had a higher grade of similarity than chondrocytes of the same individual. These results were validated using real-time PCR and immunohistochemistry.We demonstrate for the first time a reliable method for culture of chondrocytes derived from PIP joints. PIP chondrocytes show a specific gene expression pattern and could be used as tool to study cartilage degeneration in HOA. Three samples of cultured chondrocytes from knee and proximal interphalangeal finger joints were compared. Gene expression of the four most differentially regulated genes was confirmed by real-time PCR in 10 independent samples.
2016-07-03 | E-GEOD-68038 | biostudies-arrayexpress
Project description:Osteoarthritis (OA) of the hand is a common disease resulting in pain and impaired function. The pathogenesis of hand OA (HOA) is elusive and models to study it have not been described so far. Culture of chondrocytes is a model to study the development of cartilage degeneration, which is a hallmark of OA and well established in OA of the knee and hip. In the current study we investigated the feasibility human chondrocyte culture derived from proximal interphalangeal (PIP) finger joints of dissecting room cadavers. Index and middle fingers without signs of osteoarthritis were obtained from 30 cadavers using two different protocols. Hyaline cartilage from both articulating surfaces of the proximal interphalangeal (PIP) joint was harvested and digested in collagenase. Cultured chondrocytes were monitored for contamination, viability, and expression of chondrocyte specific genes. Chondrocytes derived from knee joints of the cadavers were cultured under identical conditions. Gene expression comparing chondrocytes from PIP and knee joints was carried out using Affymetrix GeneChip Human 2.0 ST arrays. The resulting differentially expressed genes were validated by real-time PCR and immunohistochemistry.Chondrocytes harvested up to 101 hours after death of the donors were viable. mRNA expression of collagen 2A1, aggrecan and Sox9 was significantly higher in chondrocytes as compared to cultured fibroblasts. Comparison of gene expression by chondrocytes from PIP and knee joints yielded 528 differentially expressed genes. Chondrocytes from the same joint region had a higher grade of similarity than chondrocytes of the same individual. These results were validated using real-time PCR and immunohistochemistry.We demonstrate for the first time a reliable method for culture of chondrocytes derived from PIP joints. PIP chondrocytes show a specific gene expression pattern and could be used as tool to study cartilage degeneration in HOA.
2016-01-01 | GSE68038 | GEO
Project description:This study investigates the transcriptomic profiles of chondrocytes under IL-1b stimulation/osteoarthritis model using high-throughput RNA sequencing. Mouse primary chondrocytes were isolated from articular cartilage of mouse knee joints and cultured under control/IL-1β treatment conditions. Total RNA was extracted and subjected to paired-end RNA-seq on the Illumina NovaSeq 6000 platform. Raw sequencing reads were processed and aligned to the GRCh38 using HISAT2. Gene expression levels were quantified as TPM and differentially expressed genes were identified using DESeq2. This dataset provides comprehensive transcriptomic insights into the molecular mechanisms underlying chondrocyte biology in the context of disease model.
2026-09-07 | GSE345836 | GEO
Project description:This study used high-throughput RNA sequencing to investigate the combination of IL-1b stimulation and IL-1b PGG-Zn@Cur Transcriptome profile of chondrocytes under pH Responsive Zn ² ⁺ - Coordinated Gellan Gum/γ - Polyglutamic Acid loaded with Curculigoside. Mouse primary chondrocytes were isolated from the articular cartilage of mouse knee joints and cultured under corresponding treatment conditions. Extract total RNA and perform paired end RNA seq on the Illumina NovaSeq 6000 platform. Use HISAT2 to process raw sequencing readings and compare them with GRCh38. The gene expression level was quantified as TPM and differentially expressed genes were identified using DESeq2. This dataset provides comprehensive transcriptomic insights into the molecular mechanisms of chondrocyte biology in the context of disease models.
2026-09-10 | GSE346645 | GEO
Project description:To evaluate sex differences of expression levels of X chromosomal genes, we performed transcriptome analysis for knee cartilage tissues and cultured finger chondrocytes.
2024-04-10 | GSE188374 | GEO
Project description: Not available
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Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:human articular cartilage from ankle, knee, and hip joints of osteoarthritis and non-osteoarthritis donors.
2024-08-23 | MSV000095686 | MassIVE
Project description: Not available
| S-EPMC5738339 | biostudies-literature
Project description:OBJECTIVE: To identify the changes in gene expression elicted by ATX inhibition in human OA primary chondrocytes. Chondrocytes were obtained from patients undergoing knee artheroplasty, cultured, and treated for 24 h with ATX inhibitor or control (without inhibitor). Total RNA was then extracted, and mRNA libraries were prepared using Illumina's TruSEQ stranded mRNA library preparation kit, pooled together, and sequenced on Illumina's NextSeq550.
2020-06-18 | GSE151937 | GEO