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Series GSE133154 Query DataSets for GSE133154
Status Public on Apr 29, 2021
Title ChIP-seq data in A673 & TC71 Ewing cell lines (STAG1 and STAG2 knock-out)
Organism Homo sapiens
Experiment type Genome binding/occupancy 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 (A673_SA2m#1, TC71_SA2m#1 and TC71_SA2m#2) derived from A673 and TC71 STAG2 wild type (WT) Ewing sarcoma cell line. Similarly, a STAG1 knock-out isogenic clone (A673_SA1m#1) was generated. Finally, a STAG2 rescue model (A673_SA2r) was generated by correcting the CRISPR mutation in the A673_SA2m#1 model. These STAG1/2 proficient and deficient models were profiled by ChIP-seq for EWS-FLI1, CTCF, cohesin members, and histone marks and allowed to highlight a global conservation of binding for these marks upon STAG2 mutation.
Overall design ChIP-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, ChIP-seq data were generated from parental A673 (WT), STAG1 KO (A673_SA1m#1), STAG2 KO (A673_SA2m#1) and STAG2 rescue models (A673_SA2r). In TC71, ChIP-seq data were generated from parental TC71 (WT) and in 2 different STAG2 KO (TC71_SA2m#1 and TC71_SA2m#2) clones generated with 2 independent sgRNAs (SA2m#1 and SA2m#2). For all these models, we performed ChIP-seq for CTCF, cohesin members (RAD21, SMC1A, STAG1 and STAG2), EWS-FLI1, H3K4m3 and H3K27ac. Respective inputs were used as normalization controls for all models.
Contributor(s) Surdez D, Zaidi S, GrossetĂȘte S, Raynal V, Baulande S, Hill V, Delattre O
Citation(s) 33930311
Submission date Jun 21, 2019
Last update date Jul 29, 2021
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 (68)
GSM3901130 A673_SA1m#1_CTCF
GSM3901131 A673_SA1m#1_FLI1
GSM3901132 A673_SA1m#1_H3K27ac
This SubSeries is part of SuperSeries:
GSE133228 STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions
BioProject PRJNA550102
SRA SRP202540

Download family Format
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Supplementary file Size Download File type/resource
GSE133154_RAW.tar 59.4 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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