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| 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
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| 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.
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| 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.
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| Contributor(s) |
Surdez D, Zaidi S, Grossetête 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
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| Department |
U830
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| Lab |
Olivier Delattre
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| Street address |
26 rue d'ulm
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| City |
Paris |
| ZIP/Postal code |
75005 |
| Country |
France |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (68)
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| This SubSeries is part of SuperSeries: |
| GSE133228 |
STAG2 promotes CTCF-anchored loop extrusion and cis-promoter and -enhancer interactions |
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| Relations |
| BioProject |
PRJNA550102 |
| SRA |
SRP202540 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE133154_RAW.tar |
59.4 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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