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| Status |
Public on Mar 01, 2019 |
| Title |
Osteoarthritis RNA Sequencing from ground cartilage samples |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Osteoarthritis (OA) is the most prevalent joint disease with the typifying feature being the progressive degradation of articular cartilage during disease progression. In this study we used whole transcriptome RNA-seq as a tool to compare gene expression changes between age-matched osteoarthritic human hip OA cartilage (n=10) compared to control (neck of femur fracture) cartilage (n=6) [GSE107308]. All cartilage was from patients undergoing acetabulofemoral joint replacement. Cartilage RNA was isolated from cartilage within 2 hr of joint replacement surgery, mRNA was polyA purified and transcript expression was analysed using 78-base paired-end sequencing generating on average 28 million reads/sample sequencing. The data shows excellent correlation with our previous microarray data but identifies significantly more differentially expressed transcripts plus novel transcript variants, several of which have been validated by real-time qPCR. Our work sheds further light on chondrocyte transcriptome expression and highlights gene expression changes and novel transcripts potentially important in osteoarthritis progression
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| Overall design |
osteoarthritic human hip cartilage (n=10) RNA was isolated from cartilage within 2 hr of joint replacement surgery, mRNA was polyA purified and transcript expression was analysed using 78-base paired-end sequencing
Please note that processed data was generated from both NOF samples (GSE107308) and OA samples.
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| Contributor(s) |
Young DA, Skelton AJ, Barter MJ |
| Citation(s) |
30611906, 29732726, 31215457 |
| |
| Submission date |
Mar 02, 2018 |
| Last update date |
Jul 02, 2019 |
| Contact name |
Andrew James Skelton |
| E-mail(s) |
andrew.skelton@ncl.ac.uk
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| Organization name |
Newcastle University
|
| Department |
Bioinformatics
|
| Lab |
Musculoskeletal Research Group
|
| Street address |
Framlington Place
|
| City |
Newcastle upon Tyne |
| State/province |
Tyne and Wear |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE111358 |
RNA-seq of Human neck of femur (NOF) fracture hip and osteoarthritic (OA) cartilage |
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| Relations |
| BioProject |
PRJNA436762 |
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