Expression data from MCF-7 breast cancer cells grown in 2D and 3D

We used a microarray to examine the global gene expression profile of MCF7 cells grown in 2D and 3D culture conditions. Our goal was to identify changes in the expression of genes that regulate iron metabolism when cellular spatial organization was altered. MCF-7 cells were grown as 2D monolayers or 3D spheroids for 3 days before RNA extraction and hybridization on Affymetrix microarrays. We used three different 3D culture methods: Poly(2-hydroxyethyl methacrylate) (pHEMA) coated U-bottom 96-well plates, Ultra-Low Attachment 96-well plates (Corning), or the additional of methylcellulose as an aggregating agent to U-bottom 96-well plates