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Series GSE116494 Query DataSets for GSE116494
Status Public on May 14, 2021
Title The effect of STAG2 loss in Ewing sarcoma [ATAC-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Ewing sarcoma is an aggressive malignancy characterized by oncogenic rearrangements of the EWS gene with an ETS-family transcription factor, most commonly FLI. Recent comprehensive next-generation sequencing efforts have revealed few other highly recurrent mutations in this disease apart from loss-of-function mutations in STAG2 which occur in 15-20% of tumors. STAG2 is a member of the cohesin complex, which regulates sister chromatid alignment during mitosis and epigenetic regulation of gene expression. While some studies suggest that loss of STAG2 is associated with the development of aneuploidy, this is not the case in Ewing sarcoma. To investigate whether STAG2 loss effects epigenetic regulation of gene expression in Ewing sarcoma, we developed isogenic Ewing sarcoma cell lines with STAG2 knockout. We found that Ewing sarcoma cells engineered for loss of STAG2 maintain an intact cohesion complex that alternately incorporates STAG1.
Overall design ATAC-seq on isogenic clonally-selected A673 cells treated with STAG2 targeting CRISPR Cas9, and on A673 cells with STAG2 wild-type. Reads mapped on the STAG2 wild-type clones (A673.sgNT-1c4 and A673.sgNT-2c3) were merged and labeled “STAG2 WT”. Reads mapped on the STAG2 knockout clones (A673.sgSTAG2-1c6, A673.sgSTAG2-4c5) were merged and labeled “STAG2 null”.
Contributor(s) Stegmaier K
Citation(s) 34129824
Submission date Jul 02, 2018
Last update date Jun 16, 2021
Contact name Gabriela Alexe
Organization name Broad Institute
Department Computational Biology and Bioinformatics
Street address 415 Main St.
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (2)
GSM3240329 ATAC-seq on A673 STAG2 WT
GSM3240330 ATAC-seq on A673 STAG2 null
This SubSeries is part of SuperSeries:
GSE116495 The effect of STAG2 loss in Ewing sarcoma
BioProject PRJNA478843
SRA SRP151748

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Supplementary file Size Download File type/resource
GSE116494_RAW.tar 305.4 Mb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data provided as supplementary file

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