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Material and Methods 
cDNA clones and microarray production
The 42,843 human cDNA genes/clones used in this study were obtained from Research Genetics (Huntsville AB, USA) (http://www.resgen.com/). This set of genes contained some redundancy (approximately 1000 genes were printed more than once on each array) and contained approximately 10,000 named genes and approximately 20,000 ESTs, hypothetical proteins, and ORFs of unknown function. The cDNA microarrays used in this study were made as previously described1,2. Detailed protocols are available at http://cmgm.stanford.edu/pbrown/array.html and http://cmgm.stanford.edu/pbrown/mguide/index.html.
RNA Isolations, Fluorescent cDNA Production and Hybridizations
Following their excision, kidneys were dissected into their component parts according to their location within the renal lobe. In addition, whole cortex was sieved to isolate glomeruli using sieves with 180 and 106um pores. Tissues were rapidly frozen in liquid N2 and then stored at -80 C until use. RNA was isolated as described in Perou et al.3, using the Trizol Reagent (Gibco-BRL)
Each of the 34 experimental samples tested here was analyzed by a comparative hybridization, using a Universal reference RNA pool (Stratagene) as a standard.

The 34 individual kidney tumor samples used in this study were collected at Stanford University in Stanford CA, USA.
A single pathologist (JPTH) reviewed H&E sections of each sample, and made a histological evaluation of each in order to exclude underlying medical renal disease. Immunohistochemistry was performed as described previously3,7.

Microarray Data Analysis
The cDNA microarrays were scanned with either an Axon (Foster City, CA) GenePix Scanner at 10 micron resolution. The output files, which were TIFF images, were then analyzed using GenePix software. Fluorescent ratios and quantitative data on spot quality were stored in the Stanford Microarray Database). Areas of the array with obvious blemishes were manually flagged and excluded from subsequent analyses. The primary data tables can be downloaded at http://genome-www.stanford.edu/microarray.

Hierarchical-clustering gene selection criteria for Figure 1
We applied average-linkage hierarchical clustering, as implemented in the program Cluster (M. Eisen; http://www.microarrays.org/software), separately to both the genes and arrays. The results were analyzed, and figures generated, using TreeView (M. Eisen; http://www.microarrays.org/software).

Supplementary Information Methods References
  1. Ross, D. T. et al. Systematic variation in gene expression patterns in human cancer cell lines [see comments]. Nat Genet 24, 227-235 (2000).
  2. Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling [see comments]. Nature 403, 503-511 (2000).
  3. Bindl, J. M. & Warnke, R. A. Advantages of detecting monoclonal antibody binding to tissue sections with biotin and avidin reagents in Coplin jars. Am J Clin Pathol 85, 490-493 (1986).

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