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Series GSE77204 Query DataSets for GSE77204
Status Public on Jul 18, 2019
Title Cell-type dependent enhancer binding of the EWS/ATF1 fusion gene in clear cell sarcomas
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Clear cell sarcoma (CCS) is a rare soft tissue sarcoma caused by the EWS/ATF1 fusion gene. Here, we established induced pluripotent stem cells (iPSCs) from EWS/ATF1-controllable murine CCS cells harboring sarcoma-associated genetic abnormalities. Sarcoma-iPSC mice develop secondary sarcomas immediately after EWS/ATF1 induction, but only in soft tissue. EWS/ATF1 expression induces oncogene-induced senescence in most cell types in sarcoma-iPSC mice but prevents it in sarcoma cells. We identify Tppp3-expressing cells in peripheral nerves as a cell-of-origin for these sarcomas. We show cell type-specific recruitment of EWS/ATF1 to enhancer regions in CCS cells. Finally, epigenetic silencing at these enhancers induces senescence and inhibits CCS cell growth through altered EWS/ATF1 binding. Together, we propose that distinct responses to premature senescence are the basis for the cell type-specificity of cancer development.
Overall design ChIP-seq was performed with mouse EWS/ATF1-induced sarcoma cell line (G1297), Ebf1- and Nanog-KRAB-introduced G1297 and sarcoma iPSC-derived MEF(sarcoma MEF). Total 9 samples (5 ChIP/ 4 input) were analized. In G1297 and its derivatives, we can induce EWS/ATF1 by Doxycycline (Dox)-inducible expression system. We compared binding pattern of EWS/ATF1 after Dox treatment between G1297 and sarcoma MEF, Ebf1-KRAB-introduced-G1297 and Nanog-KRAB-introduced G1297.
Contributor(s) Komura S, Itakura F, Yamada Y
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Submission date Jan 25, 2016
Last update date Jul 25, 2021
Contact name Yasuhiro Yamada
Organization name University of Tokyo
Department Institute of Medical Science
Lab Division of Stem Cell Pathology
Street address 4-6-1, Shirokanedai, Minato-ku
City Tokyo
ZIP/Postal code 108-8639
Country Japan
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (9)
GSM2045999 G1297 Dox ON 12h 1
GSM2046000 G1297 input DNA 1
GSM2046001 G1297 Dox ON 12h 2
This SubSeries is part of SuperSeries:
GSE77205 Cell-type dependent enhancer binding of the EWS/ATF1 fusion gene in clear cell sarcomas
BioProject PRJNA312285
SRA SRP071136

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
GSE77204_MACS-G1297-12h-HA_INT_p9_peaks.bed.txt.gz 120.3 Kb (ftp)(http) TXT
GSE77204_MACS-MEF-12h-HA_INT_p9_peaks.bed.txt.gz 398.3 Kb (ftp)(http) TXT
GSE77204_RAW.tar 12.1 Gb (http)(custom) TAR (of BW)
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Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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