Expression changes associated with siRNA-mediated down regulation of TRMT12

A microarray study was performed to identify the genes and pathways to shed light on our observation of TRMT12 overexpression in breast cancer cell lines. In this study, we compared the differential gene expression profiles of the breast cancer cell line SKbr3 treated with TRMT12 siRNA and control siRNA. RNA was extracted and linearly amplified once, then dye-labeled and co-hybridized to a microarray with over 35,000 oligos (Human Qiagen version 3 set). A 35k expression arrays were generated by printing Oligo nucleotides from the Human Qiagen version 3 set onto epoxy slides. Total RNA from SKbr3 siRNAs treated cells was amplified using an Ambion kit (Cat#1753), labeled with Cy dyes and hybridized overnight to the oligo chip in a MAUI chamber. Three different TRMT12 siRNAs were used. Each TRMT12 siRNA is compared to the same control siRNA in triplicate, including one dye swap, for a total of nine hybridizations. Please note that the data for dye-swap experiments ( hv35565, hv35568, hv35571) was reversed in the raw data already, so that the ratios are in the same direction as the first two replicates.