|
| Status |
Public on Nov 04, 2010 |
| Title |
Ankylosing spondylitis patient 9 |
| Sample type |
RNA |
| |
|
| Source name |
Whole blood, affected
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Whole blood
cell type: PBMC
disease status: Ankylosing spondylitis patient
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extracted from PAXgene tubes according to manufacturers protocol. Excess globin mRNA transcripts were removed using the Ambion GLOBINclear kit according to the manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
cRNA generated an amplified according to Illumina® TotalPrep™ RNA Amplification Kit (Ambion). 500ng of total RNA was used as starting material. A 14hr incubation was used for the in vitro transcription stage.
|
| |
|
| Hybridization protocol |
18hrs @ 58C
|
| Scan protocol |
Scanned on Illumina Beadscan according to Direct Hyb protocol
|
| Data processing |
Data processed using Lumi - data were transformed by variance stabilization transformation and normalized by robust spline normalization. In the intial study 18 patients and 18 controls were used but 2 patients and 2 controls were excluded from analysis due to samples drying out on the chip during hybridisationa dn giving aberrant fluoresence signals. This was verified during clustering analysis where these samples were clear outliers. Probes that were not expressed above background in any of the samples were removed.
ID ref = Illumina probe ID, sample values = normalised, log transformed signal intensities
|
| |
|
| Submission date |
Nov 03, 2010 |
| Last update date |
Nov 03, 2010 |
| Contact name |
Gethin Thomas |
| E-mail(s) |
[email protected]
|
| Phone |
+61 7 3176 2755
|
| Fax |
+61 7 3176 5946
|
| Organization name |
University of Queensland Diamantina Institute
|
| Street address |
Princess Alexandra Hospital
|
| City |
Woolloongabba |
| State/province |
QLD |
| ZIP/Postal code |
4102 |
| Country |
Australia |
| |
|
| Platform ID |
GPL6947 |
| Series (1) |
| GSE25101 |
Expression profiling in whole blood in ankylosing spondylitis patients and controls |
|
