Gene transcription profiling for the BN, GK, and chromosome 1 congenic strains was performed using Sentrix® BeadChip RatRef-12 v1 Whole-Genome Gene Expression Arrays (Illumina Inc., San Diego, California, USA).
Double-stranded cDNA and purified biotin-labeled cRNA were synthesized from 300 ng high quality total RNA using the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, Texas, USA). cRNA concentrations were determined using a NanoDrop spectrophotometer whilst cRNA quality and integrity were assessed using an Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany). Hybridizations onto Sentrix® BeadChip RatRef-12 v1 Arrays were carried out using 750 ng of each biotinylated cRNA in a 58°C hybridization oven for 18 hours. Following washing and staining with Streptavidin-Cy3, the BeadChip Arrays were scanned on the Illumina® BeadArray Reader (Illumina Inc., San Diego, USA). Resulting data were then preliminarily analysed using the Illumina® BeadStudio Application software before undergoing comprehensive statistical analysis.
Microarray experiments were compliant with MIAME (Minimum Information About a Microarray Experiment) and both protocol details and raw data have been deposited in ArrayExpress (http://www.ebi.ac.uk/arrayexpress/ ) under the accession number E-MTAB-1048.
Double-stranded cDNA and purified biotin-labeled cRNA were synthesized from 300 ng high quality total RNA using the Illumina® TotalPrep RNA Amplification Kit (Ambion Inc., Austin, Texas, USA). cRNA concentrations were determined using a NanoDrop spectrophotometer whilst cRNA quality and integrity were assessed using an Agilent 2100 Bioanalyser (Agilent Technologies, Waldbronn, Germany). Hybridizations onto Sentrix® BeadChip RatRef-12 v1 Arrays were carried out using 750 ng of each biotinylated cRNA in a 58°C hybridization oven for 18 hours. Following washing and staining with Streptavidin-Cy3, the BeadChip Arrays were scanned on the Illumina® BeadArray Reader (Illumina Inc., San Diego, USA). Resulting data were then preliminarily analysed using the Illumina® BeadStudio Application software before undergoing comprehensive statistical analysis.
Microarray experiments were compliant with MIAME (Minimum Information About a Microarray Experiment) and both protocol details and raw data have been deposited in ArrayExpress (