7 protocols
Summarisatiodid_not_smoke of the calls idid_not_smoke Gedid_not_smokeomeStudio versiodid_not_smoke Backgroudid_not_smoked corrected, quadid_not_smoketile did_not_smokeormalised.
Summarisation of the calls in GenomeStudio version No normalisation, no background correction.
Arrays were scanned using Illumina BeadArray Reader (part of Illumina BeadStation 500), according to the manufacturer's protocol.
1.5 microgram of cRNA per hybridisation was hybridised on Illumina HumanWG-6 v3 Expression BeadChip (Illumina, USA) according to the manufacturer's protocol (in Illumina Hybridization Oven).
150 ng of RNA was amplified and labelled using Illumina TotalPrep RNA Amplification Kit (Ambion, Austin, USA) according to the manufacturer's protocol.
Total RNA was isolated from the cryostat sections using RNeasy Micro Kit (Qiagen) and checked for integrity (RIN).
The specimen were obtained from patients suffering from HNSCC after their informed consent in full agreement with the local ethical committee based on the Declaration of Helsinki. Samples from SSC (tumour) and normal epithelium (non-neoplastic epithelium, normal) were collected from each patient. The tissue was protected by RNA-Later (Ambion Inc., Austin, TX, USA), deeply frozen in liquid nitrogen and stored at -85 degrees C to prevent activity of endogenous RNases. Frozen sections (Cryocut-E, Reichert-Jung, Vienna, Austria) were used for RNA isolation.