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Series GSE61150 Query DataSets for GSE61150
Status Public on Oct 22, 2014
Title Aberrant DNA methylation in rhabdomyosarcoma
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary Many pediatric malignancies are embryonal in nature, and one hypothesis for the origin of embryonal tumors is that they arise from a defect in differentiation, either by an inability to terminally differentiate or a reversion to a pluripotent state. There is emerging evidence that epigenetic regulation plays an important role in the transition from embryonic stem cell to a more committed cell fate, utilizing both de novo DNA methylation and poised ‘bivalent’ chromatin domains (H3K27me3 and H3K4me3) to abolish pluripotency and gain lineage- and cell-type-specific characteristics as a cell differentiates. Thus inappropriate epigenetic silencing by aberrant DNA methylation of bivalent genes required for differentiation could lead to the uncontrolled cell growth observed in cancer. Our broad hypothesis is that aberrant DNA methylation in cancer is targeted to a non-random subset of critical pathways used in normal development. This dysregulation of the normal epigenetic program used in development promotes cellular proliferation and provides a mechanism to block differentiation in pediatric cancers, such as rhabdomyosarcoma.
 
Overall design Examination of DNA methylation in fourteen human rhabdomyosarcoma patient samples using RRBS. In addition, RRBS was used to examine DNA methylation in one human rhabdomyosarcoma cell line (RD) forced to terminally differentiate by expression of the forced heterodimer MyoD~E12 (MDE). Lastly, RRBS was used to examine DNA methylation changes during normal differentiation in one primary human normal myoblast cell line
 
Contributor(s) Diede SJ, Yao Z, Rudzinski ER, Hawkins DS, Tapscott SJ
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Submission date Sep 05, 2014
Last update date May 15, 2019
Contact name Scott J. Diede
E-mail(s) scott.diede@merck.com
Organization name Fred Hutchinson Cancer Research Center
Street address 1100 Fairview Avenue North, Mailstop c3-168
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (21)
GSM1498453 FSKM
GSM1498454 NR135_MB
GSM1498455 NR135_MT
Relations
BioProject PRJNA260353
SRA SRP046229

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Supplementary file Size Download File type/resource
GSE61150_CG.sites.txt.gz 197.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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