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Sample GSM1007871 Query DataSets for GSM1007871
Status Public on Nov 15, 2012
Title 5388438026_H
Sample type RNA
 
Source name Dissected spine
Organism Mus musculus
Characteristics strain: BALB/c
genotype/variation: IL4 knockout
treatment: none (Control)
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) gethin.thomas@uq.edu.au
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

Data table header descriptions
ID_REF
VALUE transformed by variance stabilization transformation (VST) then normalized by robust spline normalization (RSN)

Data table
ID_REF VALUE
ILMN_2896528 10.32481194
ILMN_2721178 8.202220917
ILMN_3033922 8.289448738
ILMN_3092673 10.14920139
ILMN_2816356 6.754218102
ILMN_2808939 7.767307758
ILMN_2634564 7.88225174
ILMN_2737647 6.660319328
ILMN_2734484 8.071408272
ILMN_2952292 6.843493938
ILMN_2699078 6.549531937
ILMN_1213681 7.325352192
ILMN_2735413 6.520947933
ILMN_2735415 6.669135094
ILMN_2891688 8.310704231
ILMN_2637698 8.60991478
ILMN_2674228 7.510352612
ILMN_2601546 6.735164165
ILMN_1230831 6.547439575
ILMN_2848071 6.619265556

Total number of rows: 25697

Table truncated, full table size 624 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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