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Series GSE185128 Query DataSets for GSE185128
Status Public on Aug 15, 2022
Title EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (Cut&Tag III)
Sample organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
Summary Ewing sarcoma is a prototypical fusion transcription factor-associated pediatric cancer that expresses EWS/FLI or highly related fusions. EWS/FLI dysregulates transcription to induce and maintain sarcomagenesis, but the mechanisms utilized are not fully understood. We therefore sought to define the global effects of EWS/FLI on chromatin conformation and transcription in Ewing sarcoma. We found that EWS/FLI (and EWS/ERG) genomic localization is largely conserved across multiple patient-derived Ewing sarcoma cell lines. EWS/FLI binding is primarily associated with compartment activation, establishment of topologically-associated domain (TAD) boundaries, enhancer-promoter looping that involve both intra- and inter-TAD interactions, and gene activation. Importantly, local chromatin features provide the basis for transcriptional heterogeneity in regulation of direct EWS/FLI target genes across different Ewing sarcoma cell lines. These data demonstrate a key role of EWS/FLI in mediating genome-wide changes in chromatin configuration and support the notion that fusion transcription factors serve as master regulators through three-dimensional reprogramming of chromatin.
Overall design EWS/FLI knock-down with RNAi followed by rescue of EWS/FLI expression with a 3XFLAG tagged EWS/FLI cDNA construct
Contributor(s) Showpnil IA, Lessnick SL
Citation(s) 36124657
Submission date Sep 30, 2021
Last update date Oct 26, 2022
Contact name Iftekhar Ahmed Showpnil
Organization name Nationwide Children's Hospital
Department CCCBD
Lab Lessnick
Street address 700 Childrens Drive
City Columbus
State/province OH
ZIP/Postal code 43205
Country USA
This SubSeries is part of SuperSeries:
GSE185132 EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma
Reanalysis of GSM4292892
Reanalysis of GSM4292893
Reanalysis of GSM4292898
Reanalysis of GSM4292899
Reanalysis of GSM4292900
Reanalysis of GSM4292901
Reanalysis of GSM4292906
Reanalysis of GSM4292907
Reanalysis of GSM4292908
Reanalysis of GSM4292909
Reanalysis of GSM4292914
Reanalysis of GSM4292915

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
GSE185128_A673-714-H3K27ac_Enhancers_withSuper.bed.gz 181.8 Kb (ftp)(http) BED
GSE185128_A673-iEF-H3K27ac_Enhancers_withSuper.bed.gz 210.4 Kb (ftp)(http) BED
GSE185128_A673-iLuc-H3K27ac_Enhancers_withSuper.bed.gz 163.5 Kb (ftp)(http) BED 227.9 Mb (ftp)(http) BW 230.8 Mb (ftp)(http) BW 216.0 Mb (ftp)(http) BW
GSE185128_EndovsKD_Gained_Enh.bed.gz 21.1 Kb (ftp)(http) BED
GSE185128_EndovsKD_Lost_Enh.bed.gz 30.8 Kb (ftp)(http) BED
GSE185128_EndovsKD_stable_Enh.bed.gz 82.6 Kb (ftp)(http) BED
GSE185128_RescuevsKD_Gained_Enh.bed.gz 11.8 Kb (ftp)(http) BED
GSE185128_RescuevsKD_Lost_Enh.bed.gz 26.1 Kb (ftp)(http) BED
GSE185128_RescuevsKD_Stable_Enh.bed.gz 96.0 Kb (ftp)(http) BED
GSE185128_RescuevsiEF_DEnhancers_DESeq2.txt.gz 321.4 Kb (ftp)(http) TXT
GSE185128_iLucVsiEF_DEnhancers_DESeq2.txt.gz 325.1 Kb (ftp)(http) TXT
GSE185128_peaks_A673_714_H3K27ac_fdr05_idr005_meanT50_FC8.narrowPeak.gz 2.7 Mb (ftp)(http) NARROWPEAK
GSE185128_peaks_A673_iEF_H3K27ac_fdr05_idr005_meanT50_FC8.narrowPeak.gz 3.1 Mb (ftp)(http) NARROWPEAK
GSE185128_peaks_A673_iLuc_H3K27ac_fdr05_idr005_meanT50_FC8.narrowPeak.gz 2.5 Mb (ftp)(http) NARROWPEAK
Processed data are available on Series record

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