|
| Status |
Public on Jul 18, 2013 |
| Title |
PBMC_GARP_7 |
| Sample type |
RNA |
| |
|
| Source name |
PBMC_OA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: Female
age (yrs): 47
tissue: blood
tissue: PBMC
disease state: case
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit following the manufacturer's recommendations. Quality control was performed with the 2100 Bioanalyser (Agilent).
|
| Label |
biotin
|
| Label protocol |
To perform cDNA synthesis, amplification, biotin labeling, and hybridization onto the microarrays the Ambion TotalPrep-96 RNA amplification kit was used according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol with Ambion TotalPrep-96 RNA amplification kit
|
| Scan protocol |
Slides were scanned with the Illumina Beadscanner 500GX
|
| Description |
4778071026_E
PBMC_OA_mRNA
|
| Data processing |
Raw data were prepared with GenomeStudio Software (Gene Expression module v1.0), without normalization or background substraction and with imputation of missing data. Subsequently, quality control was performed in R statistical programming language using the lumi-package, and data were prepared for analysis by applying robust spline normalization (RSN) and variance-stabilizing transformation (vst)
|
| |
|
| Submission date |
Jul 09, 2013 |
| Last update date |
Jul 18, 2013 |
| Contact name |
Yolande F. M. Ramos |
| E-mail(s) |
[email protected]
|
| Organization name |
Leiden University Medical Center
|
| Department |
Molecular Epidemiology
|
| Street address |
Einthovenweg 20
|
| City |
Leiden |
| ZIP/Postal code |
2333 ZC |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE48556 |
Gene expression profiles from peripheral blood mononuclear cells (PBMCs) of osteoarthritis patients and healthy controls |
|
