Computational protocol: Nicotinamide Inhibits Vasculogenic Mimicry, an Alternative Vascularization Pathway Observed in Highly Aggressive Melanoma

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Protocol publication

[…] Whole genome expression oligonucleotide microarray analyses were carried out on HAG melanoma cell line treated with 20 mM nicotinamide (Sigma Aldrich) compared to vehicle-treated cells. Total RNA was extracted and processed using TRIzol® Reagent (Ambion, TX, USA), including phase separation by chloroform, RNA precipitation with isopropanol alcohol and RNA washing with 75% ethanol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Total RNA was used as template to generate cDNA with a High-capacity reverse transcriptase kit (Applied Biosystems) using random hexamer primers. Subsequent biotinylated target cRNA was processed by an Affymetrix GeneChip Instrument System (Affymetrix) according to manufacturer’s recommendations. The complete description of this procedure is available at: http://Affymetrix.com/support/technical/manual.affx. The differentially expressed genes were analyzed by Ingenuity Pathway Analysis (http://www.ingenuity.com) and Toppgene algorithm . Full microarray data are deposit in NCBI GEO archive. […]

Pipeline specifications

Software tools IPA, ToppGene Suite
Application Gene expression microarray analysis
Organisms Homo sapiens
Diseases Melanoma, Neoplasms
Chemicals Niacin, Niacinamide