Expression microarray analysis of monolayer versus 3D-MB cultures.

<p>(<b>A)</b> Diagram of experimental design for comparison of transcriptomes of monolayer and 3D-MB cells. OM, original monolayer; MB, melanoma bodies; NM, new monolayer. <b>(B)</b> Raw microarray data for six housekeeping genes in OM, MB and NM RNA samples: ACTB, Beta-Actin; ACTG1, Gamma 1 Actin; GAPDH, Glyceraldehyde-3-Phosphate Dehydrogenase; LDH1, Lactate Dehydrogenase; UBC, Ubiquitin C; VIM, Vimentin. An average value was calculated from 10 spots, for each gene. (<b>C)</b> Sampling of genes upregulated 5-fold or greater in the MB sample compared to the OM and NM samples (MB>OM, MB>NM). Genes are ordered according to the fold-upregulation in the MB sample versus OM sample (MB>OM). Samples were normalized versus an average of three housekeeping genes, GAPDH, ACTB and HSP90 (see Panel B), and error bars represent the standard deviation. Grey filled circles indicate genes categorized with the GO term “developmental process.” (<b>D)</b> Sampling of genes downregulated 5-fold or greater in the MB sample compared to the OM and NM samples (MBE) Venn diagram showing the number of upregulated and downregulated (unshared and shared) genes when OM, MB and NM are compared. (<b>F)</b> Heat maps of genes upregulated and downregulated in MB samples compared to OM and NM samples.