SUPPLEMENTARY DATA for ex vivo BECs and LECs as well as for optimization 1 round vs. 2 round.
	
Gene expression raw data
MIAME (Minimal Information About Microarray Experiments) criteria were fulfilled as described (Brazma et al, 2001). Briefly, the following experimental characteristics should be mentioned: 
1. Experimental design
Type of the experiment: Labeled cRNA deriving from 10µg or 15 ng total RNA from dermal BEC and LEC primary cultures was amplified in a one round and two round protocol, respectively. In addition cRNA from ex vivo microprepared BECs and LECs deriving from dermal breast skin of four healthy female donors was generated. The samples were independently hybridized to separate Affymetrix GeneChips U133A deriving from the same lot. 
The aim was investigation of BEC and LEC transcriptomes and comparison of different normalization procedures. 
The experiments are described in the following manuscript submitted to Diagnostic Molecular Pathology in February 2004:
Non-Uniform Hybridization: a Potential Source of Error in Oligonucleotide-Chip Experiments with Low Amounts of Starting Material. Nikolaus Wick, J—zsef Bruck, Elisabeth Gurnhofer, Carl-Walter Steiner, Pietro Giovanoli, Dontscho Kerjaschki and Stefan Thurner.

2. DNA-chip design
The design and characteristics of Affymetrix GeneChips U133A is described at www.affymetrix.com. 


3. Samples
Blood and lymphatic microvascular endothelial cells (BECs, LECs) were microprepared from the stratum papillare of human dermis by a protocol containing enzymatic, mechanical and immunosorting steps as described (Kriehuber et al, 2001). Total RNA of sorted BECs and LECs was isolated using an RNeasy Mini Kit (Quiagen, no. 74104). Fifteen ng total RNA was used for two round amplification protocol. Reverse transcription using oligo(dT)-T7 primers with SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen, no. 11917-010) was followed by IVT using AmpliScibe T7 Transcription Kit (Epicentre Technologies, no. AS3107). Subsequently, using random hexamers cRNA was reverse transcribed a second time with random hexamers and IVT carried out by Bio Array High Yield RNA Transcript Labeling Kit (Enzo Life Sciences Inc, no. 42655-10). Labeled cRNA samples were fragmented by heat (95¡C, 35 min.) and salt (20mM Tris-acetat (pH 8.1), 500mM KOAc, 150mM MgOAc). Prior to hybridization external control transcripts (GeneChip Eukaryotic Hybridization Control Kit, Affymetrix) including bacterial BioB at a final concentration of 3pM were added.

4. Hybridization
The hybridization solution contained 0.5 mg/ml acetylated BSA, 0.5mg/ml herring sperm DNA in 2xMES buffer. Five µg of fragmented cRNA were resuspended in 38 µl volume and added to obtain a 230 µl hybridization solution. The solution was hybridized to GeneChips Human Genome U133A for 16 hours at 45¡C using a rotating device fixed in an incubator case. Washing was done with 6xSSPE and MES buffers. Detection was done by streptavidin-phycoerythrin (SAPE) principle.

5. Scanning
Scanning was performed on a GeneChip Scanner. The hybridization scan raw data were generated as .tif files. Fluorescence intensities scaled in arbitrary units were saved as .cel files and reopened as .txt files. They can be downloaded as .txt tab-delimited files. Data were normalized using Matlab software (Wick et al., manuscript submitted to Diagnostic Molecular Pathology in February 2004) and can be downloaded as .txt tab-delimited files. At http://www.meduniwien.ac.at/complex-systems/genomics_bioinf.html the data can be downloaded.

6. Controls
Two normalization strategies were used: The default method of normalization to a predefined housekeeping gene set and the optimized method of normalization to a selected housekeeping gene subset. In addition, the control elements provided by Affymetrix (bacterial genes BioB, BioC, BioD, and Cre, as well as oligo bio-948) were considered (Wick et al., manuscript submitted to Diagnostic Molecular Pathology in February 2004).





7. References
Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, and Vingron M. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001; 29:365-371.
Kriehuber E, Breiteneder-Geleff S, Groeger M, Soleiman A, Schoppmann SF, Stingl G, Kerjaschki D, and Maurer D. Isolation and characterization of dermal lymphatic and blood endothelial cells reveal stable and functionally specialized cell lineages. J Exp Med. 2001; 194:797-808.