ABSTRACT: Comparison of mRNA expression in human EPC vs. HUVEC vs. human monocytes. Cell-type specific gene expression under basal cell culture conditions (no stimulation). The hybridization was performed with three samples of EPC vs. three samples of HUVEC vs. 3 samples of CD14+ monocytes. • The origin of the biological sample: Human endothelial progenitor cells (EPC): EPC were ex vivo cultivated from human peripheral blood-derived mononuclear cells (PBMC). PBMC were isolated by density gradient centrifugation from healthy human volunteers as previously described (Dimmeler et al., 2001). Pooled human umbilical vein endothelial cells (HUVEC) were purchased from Cambrex (Verviers, Belgium). CD14+ monocytes were purified from PBMC by positive selection with anti-CD14-microbeads (Miltenyi Biotec, Bergisch-Gladbach, Germany). Purity assessed by FACS analysis was greater than 95%. • Manipulation of biological samples and protocols used: for example, growth conditions, treatments, separation techniques: EPC: 8000000 PBMC/ml were plated on human fibronectin (Sigma, Taufkirchen, Germany) and maintained in endothelial basal medium (Cambrex) with EGM SingleQuots and 20% fetal calf serum (FCS). After 3 days, nonadherent cells were removed and adherent cells were incubated in fresh medium for 24 h before starting experiments. HUVEC: HUVEC were cultured in endothelial basal medium (Cambrex) supplemented with hydrocortisone, bovine brain extract, gentamicin, amphotericin B, epidermal growth factor, and 10% FCS until the third passage according to the manufacturer’s recommendations. CD14+ monocytes: No culture. • Protocol for preparing the hybridization extract: for example, the RNA or DNA extraction and purification protocol. Total RNA was extracted from EPC, HUVEC, and CD14+ monocytes using the RNeasy cleanup system (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Quantity and quality of total RNA was analyzed by the 2100 Bioanalyzer system (Agilent Technologies, Waldbronn, Germany) and agarose gel electrophoresis. • Labeling protocol(s): The detailed protocol for the sample preparation and microarray processing is available from Affymetrix (Santa Clara, CA). Briefly, 10 µg of purified total RNA was reverse transcribed by Superscript II reverse transcriptase (Life Technologies, Grand Island, NY) using T7-(dT)24 primer containing a T7 RNA polymerase promoter. After synthesis of the second complementary DNA (cDNA) strand, this product was used in an in vitro transcription reaction to generate biotinylated complementary RNA (cRNA). • The protocol and conditions used during hybridization, blocking and washing: Fifteen micrograms of fragmented, biotinylated cRNA were hybridized to a HG-U95Av2 microarray (Affymetrix Inc.) for 16 hours at 45° C with constant rotation at 60 rpm. This high-density oligonucleotide array targets 9,670 human genes as selected from the National Center for Biotechnology Information (NCBI) Gene Bank database with a total of 12,000 oligonucleotide sets. Each microarray was used to assay a single sample. After hybridization, the microarray was washed and stained on an Affymetrix fluidics station and scanned with an argon-ion confocal laser, with a 488 nm emission and detection at 570 nm. • GeneChip image analysis was performed using the Microarray Analysis Suite 5.0 (Affymetrix, Inc.). Expression data were analyzed utilizing the GeneSpring™ software version 4.2 (Silicon Genetics Inc., San Carlos, CA). Keywords: parallel sample
