GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE38983 Query DataSets for GSE38983
Status Public on Apr 03, 2013
Title Genome-wide analysis of mouse intestinal adenoma identifies early steps in the formation of cancer-specific DNA methylation patterns
Organism Mus musculus
Experiment type Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Aberrant CpG methylation is a universal trait of cancer cell genomes and can result in epigenetic modulation of gene activity; however, at which stages tumour-specific epigenetic patterns arise is unknown. Here, we analyse the methylome of APCM in mouse intestinal adenoma as a model of intestinal cancer initiation, and inventory a map of over 13,000 adenoma-specific recurrent differentially methylated regions (DMRs). We find that multiple genes coding for Polycomb proteins are upregulated in adenoma, and concomitantly, hypermethylated DMRs form preferentially at Polycomb target sites. We establish that DMRs are absent from proliferating intestinal epithelial cells or intestinal stem cells, and thus arise de novo after loss of APC. Importantly, a core set of DMRs is conserved in human colon cancer, defining a class of early epigenetic alterations that are distinct from known sets of epigenetically silenced tumour suppressors. The data presented suggests a sequence of events that leads to an altered methylome of colon cancer cells, and may allow more specific selection of clinical epigenetic biomarkers.
Overall design Analysis of the methylome and RNA expression in adenoma of Apc-Min/+ mutant mice and of normal intestine in Apc-Min/+ and Apc-+/+ wild type mice.
Contributor(s) Grimm C, Chavez L
Citation(s) 23408899
Submission date Jun 27, 2012
Last update date May 15, 2019
Contact name Lukas Chavez
Organization name German Cancer Research Center (DKFZ)
Street address Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
Platforms (1)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (21)
GSM953260 MeDIP_B1 (MeDIP4-4)
GSM953261 MeDIP_B2 (MeDIP4-5)
GSM953262 MeDIP_B3 (MeDIP10-1)
BioProject PRJNA169535
SRA SRP013986

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
GSE38983_RNA_MeDIP_promoter_genebody_v2.txt.gz 1.4 Kb (ftp)(http) TXT
GSE38983_hyper_500bp_Ad_vs_BN_v1.txt.gz 269.7 Kb (ftp)(http) TXT
GSE38983_hyper_DMR_merged_Ad_vs_BN_v1.txt.gz 216.6 Kb (ftp)(http) TXT
GSE38983_hypo_500bp_Ad_vs_BN_v1.txt.gz 507.4 Kb (ftp)(http) TXT
GSE38983_hypo_DMR_merged_Ad_vs_BN_v1.txt.gz 377.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap