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| Status |
Public on Jul 15, 2013 |
| Title |
A comparative gene expression profiling of spondyloarthropathy and rheumatoid arthritis using oligonucleotide based microarrays |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
|
| Summary |
Comparative gene expression profiling of mononuclear cells from synovial fluid samples of rheumatoid arthritis (RA) and
spondyloarthropathy (SpA) cases was performed. A total of 72 transcripts were found to be differentially expressed in RA compared
to SpA, with p-value threshold of 0.05 and using the Benjamini-Hochberg False Discovery rate multiple comparison corrections.
From the list, 57 transcripts were found to be upregulated in RA as compared to SpA and 15 downregulated by a fold
change cut-off of 1.5-fold.
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| Overall design |
The proposed study carried out mRNA expression profiling of mononuclear cells from synovial fluid samples of seven RA and five SpA cases. We have used 4X44K and 1X44K arrays from Agilent Technologies platform. Based on the RNA integrity, selected molecules were processed further using single-color microarray based gene expression. The raw data files obtained from this study were eventually analyzed with R package of the BioConductor suite.
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| Contributor(s) |
Pandey A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Jun 16, 2011 |
| Last update date |
Feb 22, 2018 |
| Contact name |
Akhilesh Pandey |
| E-mail(s) |
pandey@jhmi.edu, arivusudar@ibioinformatics.org, sameerkumar.iob@gmail.com, microarray@ibioinformatics.org
|
| Phone |
91 080 28416140
|
| Organization name |
Institute of Bioinformatics
|
| Street address |
UnitI, Discoverer building, ITPL
|
| City |
Bangalore |
| State/province |
Karnataka |
| ZIP/Postal code |
560 066 |
| Country |
India |
| |
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| Platforms (2) |
| GPL1708 |
Agilent-012391 Whole Human Genome Oligo Microarray G4112A (Feature Number version) |
| GPL4133 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Feature Number version) |
|
| Samples (12)
|
| GSM743016 |
Synovial fluid of Rheumatoid arthritis (RA) sample 1 |
| GSM743017 |
Synovial fluid of Rheumatoid arthritis (RA) sample 2 |
| GSM743018 |
Synovial fluid of Rheumatoid arthritis (RA) sample 3 |
| GSM743019 |
Synovial fluid of Rheumatoid arthritis (RA) sample 4 |
| GSM743020 |
Synovial fluid of Rheumatoid arthritis (RA) sample 5 |
| GSM743021 |
Synovial fluid of Rheumatoid arthritis (RA) sample 6 |
| GSM743022 |
Synovial fluid of Rheumatoid arthritis (RA) sample 7 |
| GSM743023 |
Synovial fluid of Spondyloarthritis (SpA) of sample 1 |
| GSM743024 |
Synovial fluid of Spondyloarthritis (SpA) of sample 2 |
| GSM743025 |
Synovial fluid of Spondyloarthritis (SpA) of sample 3 |
| GSM743026 |
Synovial fluid of Spondyloarthritis (SpA) of sample 4 |
| GSM743027 |
Synovial fluid of Spondyloarthritis (SpA) of sample 5 |
|
| Relations |
| BioProject |
PRJNA143705 |
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