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Sample GSM491343 Query DataSets for GSM491343
Status Public on Jan 31, 2010
Title YAC128 mouse, 24 months of age, 1692176102_F
Sample type RNA
 
Source name Mouse id 53.64.57
Organism Mus musculus
Characteristics age: 24 months
tissue: whole striatum
genotype: YAC128
Extracted molecule total RNA
Extraction protocol Striatal tissue was collected from 12 and 24 month old YAC128 mice and wildtype littermates. Animals were anaesthetized using Avertine and tissue was collected in RNAlater (Ambion) and stored at -80 prior to RNA isolation. Homogenization of tissue was performed using a Fastprep Homogenizer (ThermoScientific). Total RNA from mouse striatum was extracted using the Qiagen RNeasy mini kit and eluted in 30 microliters RNase free water according to manufacturer's instructions. Total RNA was quantified using the Nanodrop spectrophotometer (ThermoScientific) and the integrity of the total RNA was determined electrophoretically on the RNA Nano Assay Chip run on the Bioanalyzer 2100 (Agilent Tech).
Label biotin
Label protocol Biotinylated antisense RNA was generated using the Illumina Totalprep RNA amplification kit
 
Hybridization protocol According to the manufacturer's instructions.
Scan protocol According to the manufacturer's instructions using the BeadExpress platform.
Description none
Data processing The BeadStudio software was used to quantile normalize and background correct the scanned microarray image data. The data was then exported into R using the beadarray package (http://bioconductor.org/packages/2.3/bioc/html/beadarray. To avoid negative values, intensities are shifted by the sample minimum.
 
Submission date Dec 28, 2009
Last update date Dec 28, 2009
Contact name Paul Pavlidis
E-mail(s) paul@chibi.ubc.ca
Organization name University of British Columbia
Department Centre for High-Throughput Biology / Psychiatry
Street address 177 Michael Smith Laboratories 2185 East Mall
City Vancouver
State/province British Columbia
ZIP/Postal code V6T 1Z4
Country Canada
 
Platform ID GPL6333
Series (2)
GSE19676 Striatum of Huntington's disease model mice [Illumina data]
GSE19677 Striatum of Huntington's disease model mice

Data table header descriptions
ID_REF Illumina probe id
VALUE Normalized intensity

Data table
ID_REF VALUE
10181072_239_rc-S 104.5
10181072_290-S 108.1
10181072_290_rc-S 102.7
10181072_311-S 99.9
10181072_311_rc-S 102.6
10181072_418-S 100.5
10181072_418_rc-S 106.4
10181072_486-S 103.2
10181072_486_rc-S 106.2
17974913_3385-S 104.5
17974913_3385_rc-S 99.3
17974913_3999_rc-S 98.9
17974913_4071-S 100.6
17974913_4071_rc-S 99.8
17974913_4426-S 103.1
17974913_4426_rc-S 102
17974913_4962-S 97.5
17974913_4962_rc-S 100.2
18S_rRNA_X00686_301-S 2818.9
18S_rRNA_X00686_523-S 1056.4

Total number of rows: 46120

Table truncated, full table size 1187 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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