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Sample GSM1007867 Query DataSets for GSM1007867
Status Public on Nov 15, 2012
Title 5388438026_D
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 10.36704826
ILMN_2721178 8.458652496
ILMN_3033922 8.151535988
ILMN_3092673 9.729179382
ILMN_2816356 6.706081867
ILMN_2808939 8.030858994
ILMN_2634564 7.84676075
ILMN_2737647 6.631106377
ILMN_2734484 7.976691246
ILMN_2952292 6.940307617
ILMN_2699078 6.593198299
ILMN_1213681 7.323783398
ILMN_2735413 6.588117123
ILMN_2735415 6.692900181
ILMN_2891688 8.313928604
ILMN_2637698 8.827282906
ILMN_2674228 7.729461193
ILMN_2601546 6.731001854
ILMN_1230831 6.615054607
ILMN_2848071 6.698773861

Total number of rows: 25697

Table truncated, full table size 625 Kbytes.




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

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