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Series GSE132966 Query DataSets for GSE132966
Status Public on Apr 29, 2021
Title RNA-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out and proficient models and silenced for EWS-FLI1)
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary 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.
Contributor(s) Surdez D, Zaidi S, GrossetĂȘte S, Raynal V, Baulande S, Hill V, Delattre O
Citation(s) 33930311, 35565457
Submission date Jun 19, 2019
Last update date May 25, 2022
Contact name Olivier Delattre
Organization name Institut Curie
Department U830
Lab Olivier Delattre
Street address 26 rue d'ulm
City Paris
ZIP/Postal code 75005
Country France
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (29)
GSM3897548 A673_SA1m#1 rep1
GSM3897549 A673_SA1m#1 rep2
GSM3897550 A673_SA1m#1 rep3
This SubSeries is part of SuperSeries:
GSE133228 STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions
BioProject PRJNA549593
SRA SRP201842

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Supplementary file Size Download File type/resource
GSE132966_RAW.tar 9.8 Mb (http)(custom) TAR (of TAB)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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