6 mm punch skin biopsies of CTCL skin lesions were obtained and immediately snap frozen in liquid nitrogen. Tissue was powdered in liquid nitrogen (Cryo-Press, Microtec Co., Chiba, Japan) and total RNA was extracted using Trizol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
Label
SAPE
Label protocol
RNA was then labeled using the standard Affymetrix (Affymetrix Inc., Santa Clara, CA) in vitro transcription labeling protocol.
Hybridization protocol
5ug of cRNA were hybridized for 16 hours at 48 deg C using an HT Human Genome U133A array plate.
Scan protocol
The plate was scanned on a Genechip HT scanner.
Description
Gene expression data from 6mm punch biopsies of skin
Data processing
Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor. RMA data processing includes background correction, quantile normalization, and expression summarization. Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.
