Kidney Tumor Transcriptome Profiling

Gene expression profiling in 66 samples (26 conventional RCCs, 17 papillary RCCs, four chromophobe RCCs, four ROs, two collecting duct carcinomas, one mucinous and spindle cell tumor, four Wilms' tumors, one clear cell sarcoma of the kidney, one rhabdoid tumor of the kidney as well as four adult and two fetal normal kidneys) was obtained using HG-U133 Plus2.0 GeneChip oligonucleotide microarray (Affymetrix Inc.; see manufacturer's manual for detailed protocol) containing 54,675 probe sets that correspond to 38,500 genes (and > 47,400 transcripts). Total RNA was purified with Qiagen RNeasy Mini Kit (Qiagen), and the cRNA synthesis and hybridization was performed by the Genomics Core Facility of EMBL (Heidelberg, Germany). The stained arrays were scanned, and perfect match and mismatch features on the scanned microarray images were quantified using default settings in Microarray Suite 5.0 software (MAS 5.0, Affymetrix Inc.) yielding signal intensity for each probe on the array. The hybridization (raw) data have been deposited in NCBI's Gene Expression Omnibus repository http://www.ncbi.nih.gov/geo/ and are available under the accession number "GSE11151".
The robust multi-array average algorithm of R and RMA implementation in Bioconductor package http://www.bioconductor.org was used to perform preprocessing of the .CEL files, including background adjustment, quartile normalization, and summarization. Expression measurements were transformed by computing the base-two logarithm before further analysis. Relative expression profiles were generated from the individual tumor expression profiles and the mean expression values of the four individual normal adult kidney expression profiles.