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Sample GSM426791 Query DataSets for GSM426791
Status Public on Jul 14, 2009
Title GK_Adipose tissue_Replicate 3
Sample type RNA
 
Source name GK adipose tissue
Organism Rattus norvegicus
Characteristics rat id: GK_14682
strain: Goto-Kakizaki
tissue: Adipose tissue
gender: Male
age: 7 months
Treatment protocol Liver and adipose tissue samples were obtained from the rats, snap-frozen in liquid nitrogen and stored at -80oC prior to use.
Growth protocol Seven-month-old male rats from the GK (n=4) and BN (n=4) colonies (Oxford) were fed with standard laboratory chow pellets (B&K Universal, Hull, UK) and kept on a 12h light/dark cycle.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from homogenized tissue samples using TRI Reagent (Sigma, UK) following manufacturer's instructions.
Label Biotin
Label protocol Double-stranded cDNA and purified biotin-labelled cRNA were synthesised from 300ng high quality total RNA using the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, Texas, USA).
 
Hybridization protocol Hybridisation to Illumina ratRef-12 v1 (11222119_A) expression beadchips was carried out using 750ng of each biotinylated cRNA in a 58ºC hybridisation oven for 18 hours. Arrays were subsequently washed and stained with Streptavidin-Cy3.
Scan protocol Arrays were scanned on the Illumina® BeadArray Reader (Illumina Inc., San Diego, USA). Illumina® BeadStudio Application software (version 1.5.1.3) was used to check the quality of the resulting data and generate raw signal intensities.
Description 14682_GK_FAT
Data processing Raw intensity data were imported into the R statistical package for further processing. An array-specific background measure, based on the average signal from negative control probes, was subtracted from all probes on the array. Data were then transformed and normalized using the vsn2 package from BioConductor.
 
Submission date Jul 13, 2009
Last update date Jul 13, 2009
Contact name Cecilia Lindgren
E-mail(s) celi@well.ox.ac.uk
Organization name Wellcome Trust Centre for Human Genetics, University of Oxford
Street address Roosevelt Drive
City Oxford
ZIP/Postal code OX3 7BN
Country United Kingdom
 
Platform ID GPL6101
Series (2)
GSE17059 Gene expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes
GSE17060 Expression in adipose tissue and liver from a spontaneous rat model of Type 2 diabetes

Data table header descriptions
ID_REF
VALUE VSN transformed and normalized signal intensity (note – this was performed separately for each tissue)

Data table
ID_REF VALUE
ILMN_1530370 4.138326817
ILMN_1530315 3.656766785
ILMN_1530343 4.31549636
ILMN_1530298 4.080078283
ILMN_1530312 3.803039307
ILMN_1530206 4.227748204
ILMN_1530174 4.955379736
ILMN_1530328 3.988498501
ILMN_1530537 4.008209259
ILMN_1530412 4.340228635
ILMN_1530540 4.17683938
ILMN_1530418 4.829316475
ILMN_1530355 4.502838735
ILMN_1530438 5.517639424
ILMN_1530180 4.895765679
ILMN_1530219 5.454684931
ILMN_1530535 4.875528218
ILMN_1530429 3.856220053
ILMN_1530449 4.668413478
ILMN_1530434 3.048163681

Total number of rows: 22226

Table truncated, full table size 540 Kbytes.




Supplementary file Size Download File type/resource
GSM426791.txt.gz 231.8 Kb (ftp)(http) TXT
Processed data included within Sample table

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