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Series GSE165977 Query DataSets for GSE165977
Status Public on May 14, 2021
Title The effect of STAG2 loss in Ewing sarcoma [HiChIP]
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 affects 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 HiChIP SMC1A was performed for the Ewing sarcoma cell line A673 under two conditions: (1) A673 cells treated with non-targeting CRISPR Cas9 guides (STAG2 WT) and (2) A673 cells treated with STAG2-targeting CRISPR Cas9 guides (STAG2 KO). Cells treated for gene editing were clonally selected and confirmed to either express STAG2 (control condition) or have a loss of STAG2 expression (STAG2 loss condition). For the control condition, we used the cell clones A673.sgNT-1c4 and the STAG2 knockout clone A673.sgSTAG2-1c6. HiChIP was performed for each clone in duplicate. Data analysis was designed as a 2x2 comparison of differential looping for SMC1A HiChIP in A673 STAG2 KO cells vs. A673 STAG2 WT cells.
Contributor(s) Stegmaier K, Alexe G
Citation(s) 34129824
Submission date Feb 02, 2021
Last update date Jul 17, 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)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (4)
GSM5059681 HiChIP SMC1A A673 STAG2 WT Replicate 1
GSM5059682 HiChIP SMC1A A673 STAG2 WT Replicate 2
GSM5059683 HiChIP SMC1A A673 STAG2 KO Replicate 1
This SubSeries is part of SuperSeries:
GSE116495 The effect of STAG2 loss in Ewing sarcoma
BioProject PRJNA698886
SRA SRP304269

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE165977_All_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 120.4 Kb (ftp)(http) TXT
GSE165977_All_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 39.4 Kb (ftp)(http) TBI
GSE165977_All_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 120.5 Kb (ftp)(http) TXT
GSE165977_All_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 39.4 Kb (ftp)(http) TBI
GSE165977_All_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 853.0 Kb (ftp)(http) TXT
GSE165977_All_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 105.7 Kb (ftp)(http) TBI
GSE165977_All_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 856.3 Kb (ftp)(http) TXT
GSE165977_All_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 105.6 Kb (ftp)(http) TBI
GSE165977_EWSFLI1.EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 15.8 Kb (ftp)(http) TXT
GSE165977_EWSFLI1.EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 10.1 Kb (ftp)(http) TBI
GSE165977_EWSFLI1.EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 15.8 Kb (ftp)(http) TXT
GSE165977_EWSFLI1.EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 10.1 Kb (ftp)(http) TBI
GSE165977_EWSFLI1.EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 127.5 Kb (ftp)(http) TXT
GSE165977_EWSFLI1.EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 33.4 Kb (ftp)(http) TBI
GSE165977_EWSFLI1.EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 127.7 Kb (ftp)(http) TXT
GSE165977_EWSFLI1.EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 33.5 Kb (ftp)(http) TBI
GSE165977_EWSFLI1_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 20.6 Kb (ftp)(http) TXT
GSE165977_EWSFLI1_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 11.8 Kb (ftp)(http) TBI
GSE165977_EWSFLI1_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 20.6 Kb (ftp)(http) TXT
GSE165977_EWSFLI1_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 11.9 Kb (ftp)(http) TBI
GSE165977_EWSFLI1_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 160.6 Kb (ftp)(http) TXT
GSE165977_EWSFLI1_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 39.1 Kb (ftp)(http) TBI
GSE165977_EWSFLI1_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 160.7 Kb (ftp)(http) TXT
GSE165977_EWSFLI1_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 39.1 Kb (ftp)(http) TBI
GSE165977_EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 47.1 Kb (ftp)(http) TXT
GSE165977_EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 20.2 Kb (ftp)(http) TBI
GSE165977_EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 47.2 Kb (ftp)(http) TXT
GSE165977_EnhProm_Differential_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 20.2 Kb (ftp)(http) TBI
GSE165977_EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz 353.8 Kb (ftp)(http) TXT
GSE165977_EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2KO.txt.gz.tbi.gz 58.7 Kb (ftp)(http) TBI
GSE165977_EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz 354.5 Kb (ftp)(http) TXT
GSE165977_EnhProm_HighConfidence_Loops_HiChIP_SMC1A_A673_STAG2WT.txt.gz.tbi.gz 58.7 Kb (ftp)(http) TBI
GSE165977_HiChIP_SMC1A_A673_Annotated_List_Differential_Loops.xlsx 1.0 Mb (ftp)(http) XLSX
GSE165977_HiChIP_SMC1A_A673_Annotated_List_High_Confidence_Loops.xlsx 21.8 Mb (ftp)(http) XLSX
GSE165977_RAW.tar 36.3 Mb (http)(custom) TAR (of TXT)
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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