|
| Status |
Public on Jul 14, 2009 |
| Title |
BN_Liver_Replicate 4 |
| Sample type |
RNA |
| |
|
| Source name |
BN liver
|
| Organism |
Rattus norvegicus |
| Characteristics |
rat id: BN_12930
strain: Brown-Norway
tissue: Liver
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 |
12930_BN_LIVER
|
| 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 |
|
