RNA-seq data of knowk-down of STAG2 or EWSR1-FLI1 in Ewing sarcoma cell lines (siCT, siEF1 & siSA2)

STAG2, a member of cohesin, is one of the most recurrently mutated genes in human cancer. Here, we investigated STAG2 function in the context of Ewing sarcoma, an aggressive bone tumor driven by EWS-FLI1 oncogene chimeric transcription factor. Five different Ewing sarcoma cell lines were transfected with siCT or 2 different siRNAs targeting STAG2 (siSA2#6 or siSA2#8). RNA in A673 & TC71 (siSTAG2) was extracted 24, 48 and 72 hours post-transfection. RNA in EW1, CHLA-10 and CHLA-258 (siSTAG2 and siEWSR1-FLI1) was extracted 72 hours post-transfection. RNA-seq based anlayses of these experiments highligted that STAG2 knock-down alters EWSR1-FLI1 activation signature. Overall design: RNA-seq were performed in 5 different Ewing sarcoma cell lines (A673,TC71, EW1, CHLA-10 & CHLA-258). In A673 & TC71, RNA-seq data were generated for transfection with 3 siRNA (non-targeting control-siCT, siSA2#6, siSA2#8) at 3 different time points: 24h, 48h and 72h. The 3 other cell lines (EW1, CHLA-10 & CHLA-258) were also transfected at 72h with different siRNAs: siCT, siSA2#6, siSA2#8, siRNA targeting EWSR1-FLI1 fusion transcript type 1 (CHLA-10 & CHLA-258) or type 2 (EW1). RNA were extracted from all cell lines from two independent biological replicates and processed for RNA-seq.