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Series GSE61951 Query DataSets for GSE61951
Status Public on Oct 30, 2014
Title Genome-wide chromatin analysis of Ewing sarcoma (ATAC-seq)
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary We show that EWS-FLI1, an aberrant transcription factor responsible for the pathogenesis of Ewing sarcoma, reprograms gene regulatory circuits by directly inducing or directly repressing enhancers. At GGAA repeats, which lack regulatory potential in other cell types and are not evolutionarily conserved, EWS- FLI1 multimers potently induce chromatin opening, recruit p300 and WDR5, and create de novo enhancers. GGAA repeat enhancers can loop to physically interact with target promoters, as demonstrated by chromosome conformation capture assays. Conversely, EWS-FLI1 inactivates conserved enhancers containing canonical ETS motifs by displacing wild-type ETS transcription factors and abrogating p300 recruitment.
Overall design Mesenchymal stem cells (MSCs) and a Ewing sarcoma cell line (SKNMC) were analyzed by ATAC-seq. EWS-FLI1 was expressed in MSCs using a lentiviral vector (pLIV EWSFLI1 or pLIV empty vector control).

* Raw data not provided for the MSC samples. *
Contributor(s) Aryee M, Rivera M
Citation(s) 25453903
Submission date Oct 01, 2014
Last update date May 15, 2019
Contact name Martin Aryee
Organization name Massachusetts General Hospital
Department Pathology
Street address 149 13th Street
City Charlestown
State/province MA
ZIP/Postal code 02129
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (3)
GSM1517633 ATAC-Seq MSC pLIV empty
This SubSeries is part of SuperSeries:
GSE61953 Genome-wide chromatin analysis of Ewing sarcoma
BioProject PRJNA262779
SRA SRP048563

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
GSE61951_RAW.tar 762.1 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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