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Series GSE50192 Query DataSets for GSE50192
Status Public on Feb 26, 2014
Title DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Background:
DNA epigenetic modifications, such as methylation, are important regulators of tissue differentiation, contributing to processes of both development and cancer. Profiling the tissue-specific DNA methylome patterns will provide novel insights into normal and pathogenic mechanisms, as well as help in future epigenetic therapies. In this study, 17 somatic tissues from four autopsied humans were subjected to functional genome analysis using the Illumina Infinium HumanMethylation450 BeadChip, covering 486 428 CpG sites.
Only 2% of the CpGs analyzed are hypermethylated in all 17 tissue specimens; these permanently methylated CpG sites are located predominantly in gene-body regions. In contrast, 15% of the CpGs are hypomethylated in all specimens and are primarily located in regions proximal to transcription start sites. A vast number of tissue-specific differentially methylated regions are identified and considered likely mediators of tissue-specific gene regulatory mechanisms since the hypomethylated regions are closely related to known functions of the corresponding tissue. Finally, a clear inverse correlation is observed between promoter methylation within CpG islands and gene expression data obtained from publicly available databases.
This genome-wide methylation profiling study identified tissue-specific differentially methylated regions in 17 human somatic tissues. Many of the genes corresponding to these differentially methylated regions contribute to tissue-specific functions. Future studies may use these data as a reference to identify markers of perturbed differentiation and disease-related pathogenic mechanisms.
Overall design DNA methylation analysis of the total 72 tissue samples and controls was performed with the Illumina Infinium HumanMethylation450 BeadChip. The 17 post-mortem human somatic tissues used in this study were collected at the time of autopsy. Controls for unmethylated and methylated DNA were represented, respectively, by whole-genome amplified DNA from subcutaneous adipose tissue (using the GenomiPhi DNA amplification kit; GE Healthcare, Piscataway, NJ, USA) and the universal methylated human DNA standard (Zymo Research). We had two technical and two biological replicates processed by chip technique.
Contributor(s) Lokk K, Modhukur V, Rajashekar B, Märtens K, Koltšina M, Mägi R, Kolde R, Nilsson TK, Vilo J, Salumets A, Tõnisson N
Citation(s) 24690455, 27004446
Submission date Aug 26, 2013
Last update date Oct 02, 2019
Contact name Kaie Lokk
Organization name University of Tartu
Street address Riia 23
City Tartu
ZIP/Postal code 501010
Country Estonia
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (70)
GSM1215388 Adipose_abdominal_BM419/4
GSM1215389 Adipose_subcutaenous_BM419/4
GSM1215390 Splenic_artery_BM419/4
BioProject PRJNA217218

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
GSE50192_GPL13534_Matrix_raw_data.txt.gz 138.0 Mb (ftp)(http) TXT
GSE50192_GPL13534_Matrix_signal_intensities_raw_data.txt.gz 153.9 Mb (ftp)(http) TXT
GSE50192_RAW.tar 183.1 Mb (http)(custom) TAR
Processed data included within Sample table
Processed data are available on Series record

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