Ontology highlight
ABSTRACT:
PROVIDER: PRJNA981280 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR24871935_1.fastq.gz | Fastqsanger.gz | |||
| SRR24871935_2.fastq.gz | Fastqsanger.gz | |||
| SRR24871936_1.fastq.gz | Fastqsanger.gz | |||
| SRR24871936_2.fastq.gz | Fastqsanger.gz | |||
| SRR24871937_1.fastq.gz | Fastqsanger.gz |
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Project description:Owing to the limited regenerative capacity of articular cartilage, damaged cartilage does not spontaneously heal over time. Various scientific efforts have been made to improve damaged articular cartilage. Nevertheless, no single approach has achieved a promising outcome for the damaged cartilage. Meanwhile, owing to the increasing cost of drug development, drug repositioning has been actively attempted. We aimed to identify the drug that can improve the cartilage defect, using chondrogenesis related microarray data recruited from the Gene Expression Omnibus (GEO) public database. Furthermore, we attempted to experiment using cellular and animal models to verify the cartilage regeneration potential for the identified drug. To screen for drugs that promote cartilage restoring, chondrogenesis related microarray data were collected from the GEO public database. The GSE69110, GSE107649, GSE111822, and GSE116173 datasets from the GEO were used to identify cartilage differentiation-related genes. Differentially expressed genes were identified using StringTie, and drug data were extracted from the Drug-Gene Interaction database. The effect of aripiprazole on cartilage was evaluated in aripiprazole-treated adipose-derived mesenchymal stem cells (ADMSCs) and chondrocyte using qRT-PCR and 3D pellet culture. The cartilage restoring efficacy was verified in vivo by mixing it with a scaffold and introducing it into the artificially damaged cartilage of Sprague-Dawley rats. Next, mRNA was sequenced for mechanistic analysis. As a result, aripiprazole significantly increased the mRNA expression of COL2A1 and SOX9, two cartilage differentiation-related genes, and chondrogenic condensation in vitro. Moreover, it effectively promoted cartilage regeneration in the cartilage defect rat model. Analysis of mRNA sequencing data from chondrocyte treated with aripiprazole, using KEGG and GOBP, indicated that aripiprazole significantly upregulates genes associated with ribosomes and cytoplasmic translation, thus promoting chondrogenesis. In conclusion, we discovered that aripiprazole can effectively improve damaged cartilage, providing a promising approach for cartilage regeneration.
2024-12-30 | GSE271026 | GEO
Project description:These libraries represent instances of Swarm rat chondrosarcoma tumors taken from different transplantation experiments. This series also contains one non-cancerous cartilage library made from rat normal growing femoral head cartilage as a comparative data point. Keywords: other
2004-07-24 | GSE1517 | GEO
Project description:We performed RNA-Seq analysis to investigate the gene expression patterns of rat articular cartilage and xiphoid cartilage.
2021-06-17 | GSE178294 | GEO
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
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Project description:These libraries represent instances of Swarm rat chondrosarcoma tumors taken from different transplantation experiments. This series also contains one non-cancerous cartilage library made from rat normal growing femoral head cartilage as a comparative data point. Keywords: other
2004-07-24 | E-GEOD-1517 | biostudies-arrayexpress
Project description:Age as the primary rise factor could be play an important role in incidence and development of osteoarthritis. A few studies have confirmed some tissue specific lncRNA were associated with development of osteoarthritis. But if age related lncRNA would be involved in pivotal post-transcriptional gene regulation in osteoarthritis is unclear. In view of this, we have an idea that several age-related lncRNA would be screened from the rat knee cartilage at different development ages by lncRNAs Microarray analysis. We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related lncRNA during this process. The rat knee articular cartilage were selected at successive stages of the rat developmental for RNA extraction and hybridization on Affymetrix lncRNA arrays. We sought to obtain homogeneous populations of cartilage at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected cartilage according to the rat developmental stages, i.e. seven time-points: newborn (T0), youth(T1), adult (T2), early-stage elderly(T3) and latter-stage elderly(T4).
2015-03-05 | E-GEOD-66554 | biostudies-arrayexpress
Project description:Articular and growth plate cartilage have comparable structures consisting of three distinct layers of chondrocytes, suggesting similar differentiation programs and therefore similar gene expression profiles. To address this hypothesis and to explore transcriptional changes that occur during the onset of articular and growth plate cartilage divergence, we used microdissection of 10-day-old rat proximal tibial epiphyses, microarray analysis, and bioinformatics to compare gene expression profiles in individual layers of articular and growth plate cartilage. We found that many genes that were spatially upregulated in intermediate/deep zone of articular cartilage were also spatially upregulated in resting zone of growth plate cartilage (overlap greater than expected by chance, P < 0.001). Interestingly, superficial zone of articular cartilage showed an expression profile with similarities to both proliferative and hypertrophic zones of growth plate cartilage (P < 0.001 each). Additionally, significant numbers of known proliferative zone markers (3 out of 6) and hypertrophic zone markers (27 out of 126) were spatially upregulated in superficial zone compared to intermediate/deep zone (more than expected by chance, P < 0.001 each). In conclusion, we provide evidence that intermediate/deep zone of articular cartilage has a gene expression profile more similar to resting zone of growth plate cartilage, whereas superficial zone has a gene expression profile more similar to proliferative and hypertrophic zones. 10-day-old rat proximal tibial epiphyses were manually microdissected into articular cartilage superficial (SZ) and intermediate/deep (IDZ) zones and growth plate cartilage resting zone (RZ) for total RNA extraction and hybridization on Affymetrix microarrays. We used 10-day-old animals because, at this age, the secondary ossification center has recently begun to form and divides the epiphysis into articular cartilage distally and growth plate cartilage more centrally. The 4 SZ samples were taken from animals 5-8, respectively, whereas the 4 IDZ and 4 RZ samples were each taken from animals 1-2, 3-4, 5-6, and 7-8, respectively.
2014-08-16 | E-GEOD-54216 | biostudies-arrayexpress
Project description:Age as the primary rise factor could be play an important role in incidence and development of osteoarthritis. Several studies have confirmed some tissue specific microRNA were associated with development of osteoarthritis. But if age related microRNA or miRNA cluster would be involved in pivotal post-transcriptional gene regulation in osteoarthritis is unclear. In view of this, we have an idea that several age-related miRNAs would be screened from the rat knee cartilage at different development ages by miRNAs Microarray analysis. We used microarrays to detail the global programme of gene expression underlying the rat knee cartilage and identified distinct classes of age-related miRNAs during this process. The rat knee articular cartilage were selected at successive stages of the rat developmental for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous populations of cartilage at each developmental stage in order to increase the temporal resolution of expression profiles. To that end, we hand-selected cartilage according to the rat developmental stages, i.e. seven time-points: newborn (T0), childhood (T1), youth(T2), adult (T3), middle-aged (T4) early-stage elderly(T5) and latter-stage elderly(T6). The objective of the study is to identify miRNA profile of knee articular cartilage at different developmental ages in rats. Total RNA were extracted from the knee articular cartilage of Sprague-Dawley rats at postnatal day 0(T0), week1(T1), week 4(T2), mon3(T3), mon 6(T4), mon 12(T5), and mon 18(T6). The microRNA profile in the specimens was detected with the Affymetrix GeneChip® miRNA 3.0 Array.
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Project description:To investigate whether the gene expression profiles of synovial fluid mesenchymal stem cells (SF-MSCs) from rat OA knees were favorable for endogenous cartilage repair, we performed RNA sequencing for SF-MSCs from intact knees and knees 4 weeks after the pMx and sham surgery.
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