Microarray-based gene expression analysis of MDA-MB-231cells treated with platinum complex compared with untreated control

MDA-MB-231 cells were treated with a platinum complex or DMF for 96 h, after which, the total RNA was extracted from MDA-MB-231 cells using Trizol reagent (Life Technologies, Carlsbad, CA, USA) and purified with a RNeasy mini kit (Qiagen, Valencia, CA, USA). Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 50 ng total RNA by using Ambion® WT Expression Kit. Following labeling, fragmented cDNA was hybridized for 16 h at 45 °C on Clariom ™ D Assay (Human, Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450. All arrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which was installed in GeneChip® Scanner 3000 7G. The row data(.cel) were normalized by the software Transcriptome Analysis Console (TAC; Vension:4.0.1) with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as a normalization method. Values presented are log2 RMA signal intensity. In microarrays, the limma R package(vension:3.36.5) was used to filter the differentially expressed genes. Limma R used the student’s t-test to filter the two-group differentially expressed genes. Empirical Bayes moderation was used to correct the P values. The threshold set for up- and down-regulated genes was a fold change > 2.0 and a P value < 0.05.