Identification of genes regulated by knockdown of EWS-FLI1 in Ewing sarcoma cells.

EWS-FLI1 is the driver oncogene in >85% of Ewing sarcoma tumors. We used siRNA to knock down EWS-FLI1 for 48h hours in two Ewing sarcoma cell lines (EW8, TC71) to identify downstream genes and pathways affected by loss of EWS-FLI1 activity. RNAseq analysis was performed after 48 hours of treatment with a nontargeting siControl or siEWS-FLI1. We performed RNA-seq in Ewing sarcoma cell lines with 48h siRNA-mediated knockdown of EWS-FLI1 or siControl.