Transcription profiling by array of human gastric cancer cell line MC-4 treated with pPeOp against untreated controls

Microarray analysis was performed to find out differentially expressed genes in pPeOp-treated MC-4 gastric cancer cells. When MC-4 cells density reached 80%, pPeOp-treated group were added the medium containing 60 µg/mL pPeOp, while the normal group were treated with culture medium. After 24 hours’ treatment, total RNA was extracted using the TRIzol reagent. After assessed the quantification and quality of RNA (NanoDrop ND-1000, NanoDrop Technologies, Wilmington, DE, USA), RNA was hybridized to an Affymetrix 3’IVT microarray (Affymetrix, California, USA). A custom long-oligo nucleotide(60-mer) array (12×135k) was manufactured based on NimbleGen proprietary Maskless Array Synthesizer (MAS) technology. Microarrays contained 41,796 probe sets and three housekeeping genes (β-actin, Histone 3, and 18S rRNA) were used as the internal controls and their expressions signal intensity were high and consistent in the samples at different groups, confirming the reliability and accuracy of these microarrays.