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Series GSE39068 Query DataSets for GSE39068
Status Public on Oct 26, 2012
Title Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary In our study we applied a genome-wide DNA methylation analysis approach, MethylCap-seq, to map the differentially methylated regions in 24 tumor and matched normal colon samples. In total, 2687 frequently hypermethylated and 468 frequently hypomethylated regions were identified, which include potential biomarkers for CRC diagnosis. Hypermethylation in the tumor samples was enriched at CpG islands and gene promoters, while hypomethylation was distributed throughout the genome. Using epigenetic data from human embryonic stem cells, we show that frequent differentially methylated regions (DMRs) coincide with bivalent loci in human embryonic stem cells. DNA methylation is commonly thought to lead to cancer gene related silencing, however integration of publically available expression analysis shows that 75% of the frequently hypermethylation genes were most likely already lowly or not expressed in normal tissue. Collectively, our study provides genome-wide DNA methylation maps of colon cancer, comprehensive lists of DMRs, and gives further clues on the role of aberrant DNA methylation in CRC formation.
Overall design To investigate DNA methylation in CRC in a genome-wide unbiased fashion, we applied MethylCap-seq. This method involves capture of methylated DNA using the MBD domain of MeCP2, and subsequent next-generation Illumina sequencing of eluted DNA. In addition, we compared MethylCap with RNA-seq and ChIP-seq profiles of H3K4me3 and H3K27me3 for the colon cancer tumor cell line HCT116 (HCT116 WT) and the cell line of HCT116 with DNMT1 and DNMT3b knockout (HCT116 DKO).
Contributor(s) Simmer F, Brinkman AB, Assenov Y, Matarese F, Kaan A, Sabatino L, Villanueva A, Huertas D, Esteller M, Lengauer T, Bock C, Colantuoni V, Altucci L, Stunnenberg HG
Citation(s) 23079744
Submission date Jul 03, 2012
Last update date May 15, 2019
Contact name Arjen Brinkman
Organization name Radboud University, Nijmegen Center for Molecular Life Sciences
Department Molecular Biology
Lab Stunnenberg
Street address NCMLS #274, Geert Grooteplein Zuid 30
City Nijmegen
ZIP/Postal code 6525 GA
Country Netherlands
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (68)
GSM955108 MethylCap-seq_1N
GSM955109 MethylCap-seq_1T
GSM955110 MethylCap-seq_2N
BioProject PRJNA169875
SRA SRP013985

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
GSE39068_MergedPeaks_normalized_tagdensity.txt.gz 137.4 Mb (ftp)(http) TXT
GSE39068_MergedPeaks_normalized_tagdensity_add_5_samples.txt.gz 15.2 Mb (ftp)(http) TXT
GSE39068_RAW.tar 8.1 Gb (http)(custom) TAR (of BED, TXT, WIG)
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Processed data provided as supplementary file
Raw data are available in SRA
Processed data are available on Series record

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