|
| Status |
Public on Nov 15, 2012 |
| Title |
5388438026_G |
| Sample type |
RNA |
| |
|
| Source name |
Dissected spine
|
| Organism |
Mus musculus |
| Characteristics |
strain: BALB/c
genotype/variation: IL4 knockout
treatment: proteoglycan-induced spondylitis
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spines were dissected from 4 control and 4 PGISp-affected mice and flash frozen in liquid nitrogen. For the PGISp mice, only mice showing severe peripheral arthritis were selected.
RNA was extracted from the spines using Trizol as per the manufacturers protocol with the extra spin step included as recommended for bone samples then cleaned up using RNAeasy columns.
|
| Label |
Cy3
|
| Label protocol |
500ng of RNA was used in the Illumina TotalPrep cRNA Amplification Kit according to the standard protocol. Samples were hybridised to Mouse Ref-8 Expression BeadChips.
|
| |
|
| Hybridization protocol |
Standard Illumina hybridization protocol
|
| Scan protocol |
Standard Illumina scanning protocol
|
| Description |
RNA extracted from flash frozen mice spines using Trizol
|
| Data processing |
Array data were processed using the Illumina BeadStudio software then the processed data were assessed for quality control and normalised in Lumi. Analysis of gene expression patterns was performed in BRB-ArrayTools. For quality control scanned images of the arrays were visually inspected for artefacts in Illumina BeadStudio followed by the graphical analysis of density plots in Lumi. The microarray data were transformed by variance stabilization transformation (VST) then normalized by robust spline normalization (RSN). Post-normalization quality control was carried out using density plots to ensure all samples had similar distribution and variance. To reduce background noise in the data analysis all probes that were not expressed in any of the samples, i.e. whose intensity was below background in all samples, were excluded from the analysis. This did not exclude probes for genes whose expression was either “switched-on” or “switched-off”.
|
| |
|
| Submission date |
Sep 20, 2012 |
| Last update date |
Nov 15, 2012 |
| 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 |
GPL6885 |
| Series (1) |
| GSE41039 |
Control vs. PGISp spine samples |
|
