GSE132966
RNA-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out and proficient models and silenced for EWS-FLI1)
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. Using a CRISPR/Cas9 approach, we generated three STAG2 knock-out isogenic clones (A673SA2m#1, TC71SA2m#1 and TC71SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. A STAG2 rescue model (A673_SA2r) generated by correcting the CRISPR mutation in the A673SA2m#1 model was also profiled using RNA-seq. Comparison of RNA-seq data allowed highlighting a broad transcriptional modulation upon STAG2 knock-out. In addition, we compared these analyses with STAG1 knock-out A673 derived model (A673SA1m#1) and with A673 (WT) and TC71 (WT) parental cells lines transfected with siCT or siEWS-FLI1. Overall design: RNA-seq were performed in 2 different Ewing sarcoma cell lines (A673 & TC71) and their respective and derivative STAG1 and STAG2 isogenic deficient and proficient models. In A673, RNA-seq data were generated from parental A673 (WT), STAG1 KO (A673SA2m#1), STAG2 KO (A673SA2m#1) and STAG2 rescue models (A673_SA2r). In TC71, RNA-seq data were generated from parental TC71 (WT) and in 2 different STAG2 KO (TC71SA2m#1 and TC71SA2m#2) clones generated with 2 independent sgRNAs (SA2m#1 and SA2m#2). For all these models, RNA from three independent biological replicates were extracted and processed for RNA-seq. A673 and TC71 cell lines (WT) were also transfected with siRNA for 72h (non-targeting control, siCT or targeting the EWS-FLI1 fusion transcript, siEF1), RNA were extracted from both cell lines from two independent biological replicates and processed for RNA-seq.