GSE133933
Effect of fibulin-3 knockdown on malignant mesothelioma cells
Whole transcriptome comparison of mesothelioma cells transfected with control vs Fibulin-3 (EFEMP1) siRNAs. Mesothelioma cells H-226 (ATCC) and H-2595 (Harvey Pass, New York University) were transfected with two fibulin-3 or control siRNAs and collected 48h after transfection. Gene expression was quantified by RNAseq using standard procedures. The results suggest that downregulation of fibulin-3 negatively affects a PI3K/AKT-dependent gene signature involved in cell growth, adhesion, and association with the extracellular matrix. Overall design: Three independent cultures from each cell line were transfected with two previously validated fibulin-3 siRNAs or control siRNA (Hu et al., Cancer Res (2012) 72: 3873-3885). Total RNA was extracted using column purification and analyzed by RNAseq using the Illumina NSQ 500/550 Hi Output KT v2.5 (75 CYS, #20024906). Analysis of gene expression was used to determine a gene signature correlated with fibulin-3 downregulation. Design: 2 cell lines x 2 conditions per cell line x 3 independent replicates