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Series GSE185127 Query DataSets for GSE185127
Status Public on Aug 15, 2022
Title EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma (CUT&Tag II)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
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
E-mail(s) Iftekhar.Showpnil@nationwidechildrens.org
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
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (20)
GSM5606824 A673-EFEndo-CTCF-CUT&Tag 1
GSM5606825 A673-EFEndo-CTCF-CUT&Tag 2
GSM5606826 A673-EFEndo-Rabbit-IgG-CUT&Tag 1
This SubSeries is part of SuperSeries:
GSE185132 EWS/FLI mediated reprogramming of 3D chromatin promotes an altered transcriptional state in Ewing sarcoma
Relations
BioProject PRJNA767689
SRA SRP339579

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

Supplementary file Size Download File type/resource
GSE185127_A673714log2CTCFvsIgG10.bw 204.5 Mb (ftp)(http) BW
GSE185127_A673ieflog2CTCFvsIgG10.bw 201.0 Mb (ftp)(http) BW
GSE185127_A673iluclog2CTCFvsIgG10.bw 171.1 Mb (ftp)(http) BW
GSE185127_CTCF_KDb_peaks_uniq.bed.gz 1.1 Kb (ftp)(http) BED
GSE185127_CTCF_WTb_peaks_uniq.bed.gz 1.0 Kb (ftp)(http) BED
GSE185127_CTCF_stableb_peaks_uniq.bed.gz 31.0 Kb (ftp)(http) BED
GSE185127_Surdezetal2021_A673_WT_Input_sorted_dedup.bw 420.1 Mb (ftp)(http) BW
GSE185127_Surdezetal2021_A673_WT_Rad21_sorted_dedup.bw 311.9 Mb (ftp)(http) BW
GSE185127_Surdezetal2021_A673_WT_SMC1A_sorted_dedup.bw 329.6 Mb (ftp)(http) BW
GSE185127_TC71ieflog2CTCFvsIgG10.bw 154.6 Mb (ftp)(http) BW
GSE185127_TC71iluclog2CTCFvsIgG10.bw 139.9 Mb (ftp)(http) BW
GSE185127_peaks_A673_iEF_197_CTCF.narrowPeak.gz 666.1 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_A673_iEF_714_CTCF.narrowPeak.gz 680.3 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_A673_iLuc_197_CTCF.narrowPeak.gz 656.5 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_TC71_iEF_CTCF.narrowPeak.gz 681.8 Kb (ftp)(http) NARROWPEAK
GSE185127_peaks_TC71_iLuc_CTCF.narrowPeak.gz 677.2 Kb (ftp)(http) NARROWPEAK
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Raw data are available in SRA
Processed data are available on Series record

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