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Next Generation Sequencing Facilitates Quantitative Analysis of Osteoarthritis related long non-coding RNAs (LcnRNAs)

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Osteoarthritis related long non-coding RNAs (LcnRNAs)

PROVIDER: PRJNA686671 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13276973_1.fastq.gz	Fastqsanger.gz
	SRR13276973_2.fastq.gz	Fastqsanger.gz
	SRR13276974_1.fastq.gz	Fastqsanger.gz
	SRR13276974_2.fastq.gz	Fastqsanger.gz
	SRR13276975_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Osteoarthritis related long non-coding RNAs (LcnRNAs)

Project description:Purpose: LncRNAs are important moleculars in immune responses. The goals of this study are to identify osteoarthritis related lncRNAs. Methods: PBMCs from healthy control and osteoarthritis patients were collected. Then, the next-generation libraries of mRNA were prepared using VAHTS mRNA-seq v2 Library Prep Kit for Illumina® (Vazyme, Nanjing, China). The Library quality was determined by Bioanalyzer 4200 (Agilent, Santa Clara, CA, USA). Then the mRNA-seq libraries were sequenced in HiSeq ⅹ10 system (Illumina, San Diego, CA, USA) on a 150bp paired-end run. The differentially expressed lncRNAs were selected as having more than 1 fold difference in their geometrical mean expression between the compared groups and a statistically significant p-value (<0.05) by analysis of DEseq2. The GO analysis on differentially expressed lncRNAs was performed with an R package: Clusterprofiler using a p<0.05 to define statistically enriched GO categories. Results: 18 lncRNAs decreased significantly in osteoarthritis patients.

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Small non-coding RNAs in extracellular vesicles derived from equine synovial fluid and plasma in a model of equine osteoarthritis

Project description:We studied extracellular vesicles (EVs) from plasma and synovial fluid in an in vivo model of equine osteoarthritis by investigating longitudinal samples. EVs were isolated using size exclusion chromatography from plasma and synovial fluid of four horses subjected to an osteochondral fragment model of osteoarthritis at 0, 10, 35, 42, 49, 56, 63 days with relevant controls.EV RNA was extracted and subject to small RNA sequencing on an Illumina NovaSeq SP using 100bp, single end reads. After mapping against EquCab.3.0 and miRBase v22.1 differential expression analysis was undertaken with edgeRv3.28 using a quasi-likelihood negative binomial generalized log-linear model. We identified a panel of altered small non-coding RNAs.

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Microarray profiling analysis of long non-coding RNAs expression in osteoarthritis

Project description:Osteoarthritis (OA) is the most common motor system disease in aging people, characterized by matrix degradation, chondrocyte death, and osteophyte formation. OA etiology is unclear, but long noncoding RNAs (lncRNAs) that participate in numerous pathological and physiological processes may be key regulators in the onset and development of OA. Because profiling of lncRNAs and their biological function in OA is not understood, we measured lncRNA and mRNA expression profiles using high-throughput microarray to study human knee OA. We identified 2,042 lncRNAs and 2,011 mRNAs that were significantly differentially expressed in OA compared to non-OA tissue (>2.0- or <-2.0-fold change; p<0.5), including 1,137 lncRNAs that were upregulated and 905 lncRNAs that were downregulated. Also, 1,386 mRNA were upregulated and 625 mRNAs were downregulated. Gene Ontology analysis and the Kyoto Encyclopedia of Genes and Genomes was used to study the biological function enrichment of differentially expressed mRNA. Additionally, coding-non-coding gene co-expression (CNC) network construction was performed to explore the relevance of dysregulated lncRNAs and mRNAs. Finally, QPCR was used to validate chip results. In general, this study provides a preliminary database for further exploring lncRNA-related mechnisms in OA. OA cartilage were collected from 19 patients undergoing total knee joint replacement due to severe OA, and normal cartilage were collected from 11 patients (trauma, thromboangiities obliterans, or osteosarcoma, or limb amputation) without history of rheumatoid arthritis or OA

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