Genechip one cycle labeling and control reagents kit

RNA samples were prepared for hybridization using the GeneChip One-Cycle Labeling and Control Reagents kit (Affymetrix). Expression profiles were created using GeneChip Human Genome U133 Plus 2.0 Array (Affymetrix), which contains a total of 47,000 human gene transcripts and variants. Expression profiles for PNF-1 treated HMVECs at seven time points (1, 2, 4, 8, 16, 24, and 48 h) were retrieved from the Gene Expression Omnibus [9 (link)]. Data pre-processing was performed using MATLAB scripts for background subtraction, normalization, and robust multi­array analysis (RMA) summarization (Mathworks, Natick, MA, USA). p values for differential expression were calculated based on the Wilcoxon signed-rank test, and significant differentially expressed genes were selected with p values below 0.003. Replicate gene IDs were then removed and their collective p values averaged. Microarray processing resulted in between 600 and 1400 differentially expressed genes per drug treatment group. Differentially expressed genes for the seven PNF-1 time points were compared in MATLAB using the pathway compendium analysis presented previously [11 (link)]. This analysis was repeated for SC-3–141, SC-3–143, SC-3­263, VEGF, and endostatin after 24 h of treatment.